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/7769659/working'
mkdir: created directory `/scratch/stefan/7769659/working/protonate'
Storing results in /scratch/stefan/7769659/finished
Working in /scratch/stefan/7769659/working
/scratch/stefan/7769659/working /scratch/stefan/7769659

/scratch/stefan/7769659/working/protonate /scratch/stefan/7769659/working /scratch/stefan/7769659
Precomputing protomers for all compounds (pH: 7.4)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
Nov 27, 2019 6:16:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:25 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:17:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:10 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:10 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:10 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:25 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:18:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:38 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:38 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:38 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:38 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:38 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:41 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:19:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:26 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:31 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:32 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:32 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:32 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:32 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:52 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:53 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:20:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:20:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:48 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:21:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:24 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:22:54 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:07 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:08 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:27 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
Nov 27, 2019 6:23:35 PM chemaxon.calculations.clean.Clean2D clean
WARNING: Stereochemical descriptor mismatch after 2D coordinate generation
ph 7.4: 1213 protomers created
Coalesing and merging protomers
1063 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1063 protomers after new stereo-center expansion
/scratch/stefan/7769659/working /scratch/stefan/7769659

Bulk generating 3D conformations all protomers in /scratch/stefan/7769659/working/3D
mkdir: created directory `/scratch/stefan/7769659/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7769659/working/protonate/xaaaada-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'
1064 3D conformations generated for 1000 compounds

Building REAL300000078001
mkdir: created directory `/scratch/stefan/7769659/working/building'
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078001'
/scratch/stefan/7769659/working/building/REAL300000078001 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078001

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078001/0 /scratch/stefan/7769659/working/building/REAL300000078001 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1
`/scratch/stefan/7769659/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=C(CCC(=O)[O-])O2)CC1)

`REAL300000078001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078001 none CC(C)(C)C1CCN(N=CC2=CC=C(CCC(=O)[O-])O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [30, 29, 30, 30, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 7, 13, 16, 16, 1, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 6, 1, 1, 7, 7, 13, 13, 29, 29, 29, 29] 77
rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 113
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078001 none CC(C)(C)C1CCN(N=CC2=CC=C(CCC(=O)[O-])O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 61, 77, 77, 77, 29, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 11, 29, 29, 61, 61, 77, 77, 1, 1, 1, 1] 77
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 20, 21, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 269
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078001 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078001
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `/scratch/stefan/7769659/finished'
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078001/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078001
Building REAL300000078002
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078002'
/scratch/stefan/7769659/working/building/REAL300000078002 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078002

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078002/0 /scratch/stefan/7769659/working/building/REAL300000078002 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/2
`/scratch/stefan/7769659/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=C(Br)S2)CC1)

`REAL300000078002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078002 none CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=C(Br)S2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 14, 16, 16, 14, 14, 14, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 5, 1, 14, 14, 14, 14] 16
rigid atoms, others: [36, 9, 10, 11, 12, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 41
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078002 none CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=C(Br)S2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 14, 14, 16, 16, 14, 14, 14, 14, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 14, 1, 1, 1, 1] 16
rigid atoms, others: [32, 1, 34, 4, 5, 6, 7, 8, 39, 40, 19, 20, 33, 38, 37, 30, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36])
total number of confs: 36
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078002 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078002
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078002/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078002
Building REAL300000078003
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078003'
/scratch/stefan/7769659/working/building/REAL300000078003 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078003

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078003/0 /scratch/stefan/7769659/working/building/REAL300000078003 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/3
`/scratch/stefan/7769659/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CNC3=C(C(=O)[O-])C=CC=C23)CC1)

`REAL300000078003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078003 none CC(C)(C)C1CCN(N=CC2=CNC3=C(C(=O)[O-])C=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 1, 1, 1, 1, 24, 24, 24, 24] 24
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47])
total number of confs: 42
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078003 none CC(C)(C)C1CCN(N=CC2=CNC3=C(C(=O)[O-])C=CC=C23)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 24, 1, 1, 1, 1] 24
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 47, 22, 23, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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
/scratch/stefan/7769659/working/building/REAL300000078003 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078003
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078003/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078003
Building REAL300000078004
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078004'
/scratch/stefan/7769659/working/building/REAL300000078004 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078004

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078004/0 /scratch/stefan/7769659/working/building/REAL300000078004 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/4
`/scratch/stefan/7769659/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CC1)

`REAL300000078004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078004 none CC(C)(C)C1CCN(N=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 1, 1, 1, 14, 14, 14, 14] 14
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 29
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078004 none CC(C)(C)C1CCN(N=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 1, 1, 1, 1] 14
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 22, 23, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42])
total number of confs: 38
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078004 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078004
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078004/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078004
Building REAL300000078005
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078005'
/scratch/stefan/7769659/working/building/REAL300000078005 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078005

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078005/0 /scratch/stefan/7769659/working/building/REAL300000078005 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/5
`/scratch/stefan/7769659/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CC1)

`REAL300000078005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078005 none CC(C)(C)C1CCN(N=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 12, 12, 12, 12] 12
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 26
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078005 none CC(C)(C)C1CCN(N=CC2=CC=CN3C(C(=O)[O-])=CN=C23)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 1, 1, 1, 1] 12
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 22, 23, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42])
total number of confs: 33
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078005 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078005
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078005/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078005
Building REAL300000078006
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078006'
/scratch/stefan/7769659/working/building/REAL300000078006 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078006

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078006/0 /scratch/stefan/7769659/working/building/REAL300000078006 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/6
`/scratch/stefan/7769659/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=CC(F)=C2C(=O)[O-])CC1)

`REAL300000078006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078006 none CC(C)(C)C1CCN(N=CC2=CC=CC(F)=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 14, 16, 16, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 4, 1, 1, 1, 14, 14, 14, 14] 16
rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 40
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078006 none CC(C)(C)C1CCN(N=CC2=CC=CC(F)=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 16, 16, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 14, 14, 14, 1, 1, 1, 1] 16
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 41, 42, 7, 40, 20, 21, 43, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 36
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078006 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078006
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078006/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078006
Building REAL300000078007
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078007'
/scratch/stefan/7769659/working/building/REAL300000078007 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078007

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078007/0 /scratch/stefan/7769659/working/building/REAL300000078007 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/7
`/scratch/stefan/7769659/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CC1)

`REAL300000078007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078007 none CC(C)(C)C1CCN(N=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 77, 77, 77, 77, 77, 77, 77, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 30, 30, 77, 77, 15, 15, 15, 15] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 16, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 182
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078007 none CC(C)(C)C1CCN(N=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 10, 10, 15, 15, 15, 15, 15, 15, 53, 142, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15, 142, 142, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [1, 4, 5, 6, 39, 38, 41, 7, 54, 40, 51, 52, 53, 8, 26, 27, 37] set([0, 2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 556
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078007 none CC(C)(C)C1CCN(N=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 88, 88, 77, 77, 77, 77, 77, 77, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 77, 77, 77, 77, 7, 7, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [49, 50, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54])
total number of confs: 333
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078007 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078007
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078007/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078007
Building REAL300000078008
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078008'
/scratch/stefan/7769659/working/building/REAL300000078008 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078008

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078008/0 /scratch/stefan/7769659/working/building/REAL300000078008 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/8
`/scratch/stefan/7769659/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=CC(Br)=C2C(=O)[O-])CC1)

`REAL300000078008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078008 none CC(C)(C)C1CCN(N=CC2=CC=CC(Br)=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 9, 9, 9, 9] 9
rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43])
total number of confs: 20
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078008 none CC(C)(C)C1CCN(N=CC2=CC=CC(Br)=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 9, 9, 9, 1, 1, 1, 1] 9
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 41, 42, 7, 40, 20, 21, 43, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 21
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078008 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078008
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078008/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078008
Building REAL300000078009
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078009'
/scratch/stefan/7769659/working/building/REAL300000078009 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078009

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078009/0 /scratch/stefan/7769659/working/building/REAL300000078009 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/9
`/scratch/stefan/7769659/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CC1)

`REAL300000078009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078009 none CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 23, 25, 25, 23, 23, 23, 8, 8, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 23, 8, 1, 1, 1, 1, 23, 23, 23, 23] 25
rigid atoms, others: [39, 40, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 55
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078009 none CC(C)(C)C1CCN(N=CC2=C(C(=O)[O-])C=CC3=C2OCO3)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 9, 9, 23, 23, 25, 25, 23, 23, 23, 23, 23, 23, 23, 1, 1, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 1, 1, 1, 1] 25
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 22, 23, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42])
total number of confs: 56
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078009 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078009
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078009/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078009
Building REAL300000078010
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078010'
/scratch/stefan/7769659/working/building/REAL300000078010 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078010

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078010/0 /scratch/stefan/7769659/working/building/REAL300000078010 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/10
`/scratch/stefan/7769659/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC(C#N)=CC=C2C(=O)[O-])CC1)

`REAL300000078010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078010 none CC(C)(C)C1CCN(N=CC2=CC(C#N)=CC=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 15, 17, 17, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15, 15] 17
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44])
total number of confs: 41
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078010 none CC(C)(C)C1CCN(N=CC2=CC(C#N)=CC=C2C(=O)[O-])CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 17, 17, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 15, 15, 15, 1, 1, 1, 1] 17
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 41, 42, 7, 44, 43, 21, 22, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 37
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078010 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078010
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078010/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078010
Building REAL300000078011
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078011'
/scratch/stefan/7769659/working/building/REAL300000078011 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078011

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078011/0 /scratch/stefan/7769659/working/building/REAL300000078011 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/11
`/scratch/stefan/7769659/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CC1)

`REAL300000078011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078011 none CC(C)(C)C1CCN(N=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 45, 49, 49, 45, 45, 45, 9, 9, 1, 1, 1, 1, 1, 1, 9, 42, 70, 70, 1, 1, 1, 45, 45, 49, 49, 49, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 9, 1, 1, 42, 42, 1, 45, 45, 45, 45] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45, 46, 47])
total number of confs: 310
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078011 none CC(C)(C)C1CCN(N=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 11, 45, 45, 40, 45, 129, 201, 201, 201, 45, 45, 45, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 11, 45, 45, 201, 201, 45, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 47, 22, 23, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43])
total number of confs: 553
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078011 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078011
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078011/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078011
Building REAL300000078012
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078012'
/scratch/stefan/7769659/working/building/REAL300000078012 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078012

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078012/0 /scratch/stefan/7769659/working/building/REAL300000078012 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/12
`/scratch/stefan/7769659/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)CC1)

`REAL300000078012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078012 none CC(C)(C)C1CCN(N=CC2=CC=C(S(=O)(=O)NCC(=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', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 1, 1, 9, 14, 14, 1, 1, 18, 18, 18, 18] 65
rigid atoms, others: [9, 10, 11, 12, 13, 14, 47, 46, 22, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 48, 49, 50, 51])
total number of confs: 79
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078012 none CC(C)(C)C1CCN(N=CC2=CC=C(S(=O)(=O)NCC(=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', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 11, 11, 18, 18, 18, 18, 30, 30, 30, 55, 65, 65, 65, 18, 18, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 11, 18, 18, 55, 65, 65, 18, 18, 1, 1, 1, 1] 65
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 39, 48, 49, 50, 51, 24, 25, 38, 37, 36] set([0, 2, 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, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 262
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078012 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078012
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078012/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078012
Building REAL300000078013
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078013'
/scratch/stefan/7769659/working/building/REAL300000078013 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078013

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078013/0 /scratch/stefan/7769659/working/building/REAL300000078013 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/13
`/scratch/stefan/7769659/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NN2CCC(C(C)(C)C)CC2)=C1C(=O)[O-])

`REAL300000078013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078013 none CC1=NSC(C=NN2CCC(C(C)(C)C)CC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 14, 14, 16, 16, 14, 14, 14, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 16
rigid atoms, others: [6, 7, 8, 9, 10, 11, 15, 16, 40, 42, 41, 25, 26, 27, 28, 29, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 50
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078013 none CC1=NSC(C=NN2CCC(C(C)(C)C)CC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 3, 3, 14, 14, 14, 14, 16, 16, 16, 14, 14, 1, 1, 3, 3, 2, 2, 2, 3, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 44
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078013 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078013
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078013/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078013
Building REAL300000078014
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078014'
/scratch/stefan/7769659/working/building/REAL300000078014 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078014

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078014/0 /scratch/stefan/7769659/working/building/REAL300000078014 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/14
`/scratch/stefan/7769659/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CC1)

`REAL300000078014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078014 none CC(C)(C)C1CCN(N=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 1, 1, 1, 25, 25, 25, 25] 25
rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 47
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078014 none CC(C)(C)C1CCN(N=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 25, 25, 25, 1, 1, 1, 1] 25
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 43, 44, 45, 46, 23, 24, 36, 38, 37] set([0, 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, 39, 40, 41, 42])
total number of confs: 43
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078014 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078014
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078014/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078014
Building REAL300000078015
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078015'
/scratch/stefan/7769659/working/building/REAL300000078015 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078015

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078015/0 /scratch/stefan/7769659/working/building/REAL300000078015 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/15
`/scratch/stefan/7769659/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NN1CCC(C(C)(C)C)CC1)

`REAL300000078015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078015 none COC1=CC(C(=O)[O-])=CC=C1C=NN1CCC(C(C)(C)C)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 29, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 29
rigid atoms, others: [32, 33, 34, 44, 45, 12, 13, 14, 15, 16, 17, 21, 22, 46, 47, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 46
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078015 none COC1=CC(C(=O)[O-])=CC=C1C=NN1CCC(C(C)(C)C)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 1, 1, 1, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 26, 27, 28] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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
/scratch/stefan/7769659/working/building/REAL300000078015 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078015
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078015/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078015
Building REAL300000078016
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078016'
/scratch/stefan/7769659/working/building/REAL300000078016 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078016

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078016/0 /scratch/stefan/7769659/working/building/REAL300000078016 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/16
`/scratch/stefan/7769659/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCN(N=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CC1)

`REAL300000078016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078016 none CC(C)(C)C1CCN(N=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 52, 58, 58, 52, 52, 52, 9, 9, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 24, 24, 13, 1, 1, 52, 52, 58, 58, 58, 58, 58, 58, 58, 58, 58, 52, 52, 52, 52, 52, 9, 13, 13, 13, 13, 1, 1, 52, 52, 52, 52] 146
rigid atoms, others: [9, 10, 11, 12, 13, 46, 45, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50])
total number of confs: 177
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078016 none CC(C)(C)C1CCN(N=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 145, 145, 145, 145, 145, 146, 146, 145, 52, 52, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 11, 145, 145, 145, 145, 52, 52, 1, 1, 1, 1] 146
rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 39, 47, 48, 49, 50, 24, 25, 38, 37, 36] set([0, 2, 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, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 320
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078016 none CC(C)(C)C1CCN(N=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 145, 146, 146, 145, 145, 145, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 13, 145, 145, 146, 146, 146, 146, 146, 146, 146, 146, 146, 145, 145, 145, 145, 145, 55, 1, 1, 1, 1, 13, 13, 145, 145, 145, 145] 146
rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50])
total number of confs: 258
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078016 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078016
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078016/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078016
Building REAL300000078017
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078017'
/scratch/stefan/7769659/working/building/REAL300000078017 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078017

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078017/0 /scratch/stefan/7769659/working/building/REAL300000078017 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/17
`/scratch/stefan/7769659/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])=N1)

`REAL300000078017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078017 none CN1C=CC(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 17, 1, 1, 1, 12, 5, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 58, 39, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 54, 54, 58, 58, 58, 58, 58, 58, 8, 8, 1, 1, 1, 35, 35] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 276
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078017 none CN1C=CC(N=NCC2=CC(Br)=CC=C2OCC(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 17, 1, 1, 1, 12, 5, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 19, 58, 58, 58, 38, 58, 58, 58, 137, 201, 201, 201, 1, 2, 2, 2, 1, 1, 18, 19, 58, 58, 58, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 660
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078017 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078017/1 /scratch/stefan/7769659/working/building/REAL300000078017 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/18
`/scratch/stefan/7769659/working/3D/18' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=N1)

`REAL300000078017.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078017/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078017 none CN1C=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [35, 35, 35, 35, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 38, 38, 35, 35, 35, 35, 35, 35, 22, 4, 1, 1, 1, 30, 30] 70
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078017 none CN1C=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 20, 20, 35, 35, 35, 20, 35, 35, 35, 59, 70, 70, 70, 1, 2, 2, 2, 1, 1, 5, 20, 35, 35, 35, 70, 70] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078017 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078017
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078017/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078017/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078017
Building REAL300000078018
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078018'
/scratch/stefan/7769659/working/building/REAL300000078018 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078018

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078018/0 /scratch/stefan/7769659/working/building/REAL300000078018 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/19
`/scratch/stefan/7769659/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1)

`REAL300000078018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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: [97, 97, 97, 97, 58, 58, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 6, 7, 7, 7, 9, 9, 1, 97, 97, 97, 97, 97, 97, 8, 8, 1, 1, 1, 2, 2, 7, 7, 6, 7, 1] 201
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 19, 97, 97, 97, 97, 97, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 97, 1, 2, 2, 2, 1, 1, 19, 18, 97, 97, 97, 136, 136, 201, 201, 201, 201, 97] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 347
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 166, 166, 43, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 201, 201, 201, 201, 201, 201, 43, 43, 7, 6, 7, 4, 4, 1, 1, 1, 1, 7] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 384
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078018 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078018/1 /scratch/stefan/7769659/working/building/REAL300000078018 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/20
`/scratch/stefan/7769659/working/3D/20' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1)

`REAL300000078018.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078018/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 8, 21, 21, 20, 21, 21, 21, 23, 23, 1, 31, 31, 31, 31, 31, 31, 24, 6, 1, 1, 1, 8, 8, 21, 21, 20, 21, 1] 82
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 130
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 15, 15, 31, 31, 31, 31, 31, 46, 52, 82, 82, 82, 82, 82, 82, 82, 82, 31, 1, 2, 2, 2, 1, 1, 3, 15, 31, 31, 31, 52, 52, 82, 82, 82, 82, 31] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 145
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078018 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 82, 73, 51, 51, 21, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 21, 82, 82, 82, 82, 82, 82, 73, 51, 21, 20, 21, 6, 6, 1, 1, 1, 1, 21] 82
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 211
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078018 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078018
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078018/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078018/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078018
Building REAL300000078019
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078019'
/scratch/stefan/7769659/working/building/REAL300000078019 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078019

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078019/0 /scratch/stefan/7769659/working/building/REAL300000078019 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/21
`/scratch/stefan/7769659/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=N1)

`REAL300000078019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078019 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 12, 12, 12, 12, 12, 12, 12, 7, 1, 1, 5, 5, 1] 15
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078019 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 6, 6, 12, 12, 10, 10, 15, 15, 15, 15, 12, 12, 12, 12, 12, 1, 2, 2, 2, 1, 1, 2, 6, 12, 12, 15, 15, 12] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 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: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078019 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078019
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078019/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078019
Building REAL300000078020
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078020'
/scratch/stefan/7769659/working/building/REAL300000078020 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078020

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078020/0 /scratch/stefan/7769659/working/building/REAL300000078020 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/22
`/scratch/stefan/7769659/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NN(C)C=C3)C=C2)=C1)

`REAL300000078020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 87, 87, 87, 87, 87, 1, 1, 8, 8, 8, 8, 1, 1, 1, 1, 9, 9, 87, 87, 87, 87, 87, 1, 1, 8] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 40, 41, 23, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 42])
total number of confs: 184
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 8, 47, 152, 152, 201, 201, 201, 201, 201, 8, 8, 1, 2, 2, 2, 8, 8, 8, 8, 47, 47, 201, 201, 201, 201, 201, 7, 8, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 409
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 87, 87, 43, 19, 87, 87, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 201, 87, 87, 87, 87, 18, 19, 2, 2, 2, 1, 1, 87, 87, 201] 201
rigid atoms, others: [38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 537
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078020 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078020/1 /scratch/stefan/7769659/working/building/REAL300000078020 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/23
`/scratch/stefan/7769659/working/3D/23' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=NN(C)C=C3)C=C2)=C1)

`REAL300000078020.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078020/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 47, 47, 27, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 37, 58, 58, 58, 58, 58, 1, 1, 27, 27, 27, 27, 7, 7, 1, 1, 9, 37, 58, 58, 58, 58, 58, 1, 1, 27] 201
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 40, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42])
total number of confs: 248
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 27, 27, 27, 27, 27, 104, 104, 183, 201, 201, 201, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 104, 183, 201, 201, 201, 201, 201, 26, 27, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 548
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078020 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=NN(C)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 88, 58, 38, 38, 58, 58, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 88, 88, 58, 58, 25, 5, 2, 2, 2, 1, 1, 58, 58, 201] 201
rigid atoms, others: [38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 463
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078020 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078020
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078020/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078020/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078020
Building REAL300000078021
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078021'
/scratch/stefan/7769659/working/building/REAL300000078021 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078021

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078021/0 /scratch/stefan/7769659/working/building/REAL300000078021 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/24
`/scratch/stefan/7769659/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1)

`REAL300000078021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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: [57, 57, 57, 57, 37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 11, 11, 11, 10, 1, 57, 57, 57, 57, 57, 57, 7, 7, 1, 1, 1, 2, 2, 11, 10, 10, 11, 1] 201
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 17, 57, 57, 57, 57, 57, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 57, 1, 2, 2, 2, 1, 1, 17, 16, 57, 57, 57, 92, 92, 201, 201, 201, 201, 57] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(N=NCC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 201, 201, 176, 176, 66, 11, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 201, 201, 201, 201, 201, 201, 66, 66, 10, 10, 10, 5, 5, 1, 1, 1, 1, 11] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 443
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078021 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078021/1 /scratch/stefan/7769659/working/building/REAL300000078021 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/25
`/scratch/stefan/7769659/working/3D/25' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1)

`REAL300000078021.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078021/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.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, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 8, 26, 26, 26, 26, 27, 27, 27, 26, 1, 35, 35, 35, 35, 35, 35, 26, 10, 1, 1, 1, 8, 8, 27, 27, 26, 27, 1] 201
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 136
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.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, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 15, 15, 35, 35, 35, 35, 35, 50, 61, 201, 201, 201, 201, 201, 201, 201, 201, 35, 1, 2, 2, 2, 1, 1, 5, 15, 35, 35, 35, 61, 61, 201, 201, 201, 201, 35] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 319
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078021 none CN1C=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.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, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 173, 120, 120, 27, 26, 26, 26, 26, 16, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 201, 201, 201, 201, 201, 201, 173, 120, 26, 26, 27, 8, 8, 1, 1, 1, 1, 27] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 529
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078021 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078021
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078021/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078021/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078021
Building REAL300000078022
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078022'
/scratch/stefan/7769659/working/building/REAL300000078022 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078022

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078022/0 /scratch/stefan/7769659/working/building/REAL300000078022 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/26
`/scratch/stefan/7769659/working/3D/26' -> `0.mol2'
Preparing input files

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

`REAL300000078022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078022 none COC1=CC=C(CN=NC2=NN(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 30, 61, 61, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 61, 61, 137, 193, 199, 199, 61, 71, 71, 71, 61, 61, 18, 19, 2, 2, 2, 1, 1, 193, 193, 61] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 685
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078022 none COC1=CC=C(CN=NC2=NN(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 38, 39, 61, 61, 61, 61, 61, 1, 1, 7, 30, 54, 54, 1, 3, 3, 3, 1, 1, 6, 6, 61, 61, 61, 61, 61, 30, 30, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 21, 25, 26, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078022 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078022/1 /scratch/stefan/7769659/working/building/REAL300000078022 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/27
`/scratch/stefan/7769659/working/3D/27' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=NN(C)C=C2)C(OCC(=O)[O-])=C1)

`REAL300000078022.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078022/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078022 none COC1=CC=C(C=NNC2=NN(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 45, 25, 45, 45, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 45, 45, 115, 184, 189, 189, 45, 68, 68, 68, 45, 45, 25, 5, 2, 2, 2, 1, 1, 184, 184, 45] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 676
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078022 none COC1=CC=C(C=NNC2=NN(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 22, 45, 45, 45, 45, 45, 1, 1, 9, 40, 78, 78, 1, 3, 3, 3, 1, 1, 5, 22, 45, 45, 45, 45, 45, 40, 40, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 21, 25, 26, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 339
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078022 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078022
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078022/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078022/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078022
Building REAL300000078023
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078023'
/scratch/stefan/7769659/working/building/REAL300000078023 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078023

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078023/0 /scratch/stefan/7769659/working/building/REAL300000078023 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/28
`/scratch/stefan/7769659/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1)

`REAL300000078023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078023 none CN1C=CC(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 21, 5, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 37, 37, 1, 1, 25, 25, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 165
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078023 none CN1C=CC(N=NCC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 11, 25, 25, 11, 11, 127, 191, 191, 191, 199, 199, 25, 25, 1, 2, 2, 2, 1, 1, 11, 11, 25, 25, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078023 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078023/1 /scratch/stefan/7769659/working/building/REAL300000078023 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/29
`/scratch/stefan/7769659/working/3D/29' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1)

`REAL300000078023.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078023/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078023 none CN1C=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 19, 4, 4, 1, 1, 1, 1, 1, 1, 12, 53, 53, 53, 82, 82, 1, 1, 32, 32, 32, 32, 32, 32, 19, 4, 1, 1, 1, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 346
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078023 none CN1C=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 20, 20, 32, 32, 20, 20, 101, 201, 201, 201, 201, 201, 32, 32, 1, 2, 2, 2, 1, 1, 5, 20, 32, 32, 32, 32] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 653
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078023 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078023
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078023/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078023/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078023
Building REAL300000078024
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078024'
/scratch/stefan/7769659/working/building/REAL300000078024 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078024

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078024/0 /scratch/stefan/7769659/working/building/REAL300000078024 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/30
`/scratch/stefan/7769659/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=N1)

`REAL300000078024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078024 none CN1C=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', '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, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 16, 8, 1, 2, 2, 2] 19
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078024 none CN1C=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', '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, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 1, 1, 5, 13, 19, 19, 19, 19] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078024 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078024/1 /scratch/stefan/7769659/working/building/REAL300000078024 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/31
`/scratch/stefan/7769659/working/3D/31' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)=N1)

`REAL300000078024.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078024/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078024 none CN1C=CC(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'N.2', '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, 17, 1, 1, 1, 11, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 8, 8, 1, 2, 2, 2] 61
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078024 none CN1C=CC(N=NCC2=C(Br)C=C(C(=O)[O-])N2C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'N.2', '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, 17, 1, 1, 1, 11, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 7, 7, 18, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 2, 2, 2, 1, 1, 17, 18, 61, 61, 61, 61] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078024 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078024
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078024/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078024/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078024
Building REAL300000078025
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078025'
/scratch/stefan/7769659/working/building/REAL300000078025 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078025

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078025/0 /scratch/stefan/7769659/working/building/REAL300000078025 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/32
`/scratch/stefan/7769659/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1)

`REAL300000078025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078025 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 43, 9, 9, 1, 1, 1, 1, 1, 1, 9, 45, 65, 65, 1, 1, 1, 66, 66, 66, 66, 66, 66, 43, 9, 1, 1, 45, 45, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 340
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078025 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 25, 25, 66, 66, 40, 66, 146, 201, 201, 201, 66, 66, 66, 1, 2, 2, 2, 1, 1, 5, 25, 66, 66, 201, 201, 66] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 600
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078025 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078025/1 /scratch/stefan/7769659/working/building/REAL300000078025 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/33
`/scratch/stefan/7769659/working/3D/33' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1)

`REAL300000078025.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078025/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078025 none CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', '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, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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: [81, 81, 81, 81, 54, 54, 8, 1, 1, 1, 1, 1, 1, 7, 21, 25, 25, 1, 1, 1, 81, 81, 81, 81, 81, 81, 8, 8, 1, 1, 21, 21, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078025 none CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Br)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', '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, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 19, 81, 81, 33, 81, 171, 201, 201, 201, 81, 81, 81, 1, 2, 2, 2, 1, 1, 18, 19, 81, 81, 201, 201, 81] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 623
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078025 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078025
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078025/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078025/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078025
Building REAL300000078026
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078026'
/scratch/stefan/7769659/working/building/REAL300000078026 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078026

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078026/0 /scratch/stefan/7769659/working/building/REAL300000078026 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/34
`/scratch/stefan/7769659/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NN(C)C=C2)C=C1)

`REAL300000078026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078026 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NN(C)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 37, 37, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 23, 9, 2, 2, 2, 1, 1, 37, 37] 37
rigid atoms, others: [32, 33, 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, 34, 35])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078026 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=NN(C)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 12, 12, 28, 37, 37, 37, 37, 37, 1, 1, 3, 3, 3, 1, 12, 28, 37, 37, 37, 37, 37, 1, 1] 37
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 21, 22, 26] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078026 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078026
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078026/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078026
Building REAL300000078027
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078027'
/scratch/stefan/7769659/working/building/REAL300000078027 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078027

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078027/0 /scratch/stefan/7769659/working/building/REAL300000078027 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/35
`/scratch/stefan/7769659/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1)

`REAL300000078027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 9, 29, 37, 112, 112, 112, 112, 112, 112, 112, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 29, 29, 37, 37, 112, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 41, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 2, 6, 6, 17, 17, 9, 17, 80, 139, 155, 201, 201, 201, 201, 201, 201, 201, 17, 17, 17, 1, 2, 2, 2, 1, 1, 2, 6, 17, 17, 139, 139, 155, 155, 201, 17] 201
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])
total number of confs: 592
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 193, 191, 74, 56, 112, 112, 56, 16, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 185, 112, 112, 16, 16, 8, 8, 1, 112] 201
rigid atoms, others: [40, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41])
total number of confs: 706
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078027 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078027/1 /scratch/stefan/7769659/working/building/REAL300000078027 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/36
`/scratch/stefan/7769659/working/3D/36' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1)

`REAL300000078027.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078027/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(N=NCC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 35, 34, 34, 6, 1, 1, 1, 1, 1, 1, 5, 15, 15, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 35, 35, 35, 35, 35, 35, 6, 6, 1, 1, 15, 15, 15, 15, 44, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 41, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(N=NCC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 8, 35, 35, 24, 35, 103, 137, 137, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 1, 2, 2, 2, 1, 1, 8, 8, 35, 35, 137, 137, 137, 137, 201, 35] 201
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])
total number of confs: 507
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078027 none CN1C=CC(N=NCC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 201, 201, 142, 30, 26, 44, 44, 24, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 44, 44, 44, 201, 201, 201, 201, 201, 201, 142, 142, 44, 44, 6, 6, 6, 6, 1, 44] 201
rigid atoms, others: [40, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078027 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078027
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078027/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078027/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078027
Building REAL300000078028
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078028'
/scratch/stefan/7769659/working/building/REAL300000078028 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078028

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078028/0 /scratch/stefan/7769659/working/building/REAL300000078028 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/37
`/scratch/stefan/7769659/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NN(C)C=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000078028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078028 none COC1=CC(C=NNC2=NN(C)C=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 37, 37, 37, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 92, 111, 111, 111, 66, 66, 66, 37, 19, 5, 2, 2, 2, 1, 1, 37, 111, 111] 111
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 307
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078028 none COC1=CC(C=NNC2=NN(C)C=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 7, 7, 27, 37, 37, 37, 37, 37, 1, 1, 2, 2, 1, 1, 1, 9, 17, 23, 23, 3, 3, 3, 1, 7, 27, 37, 37, 37, 37, 37, 1, 17, 17] 111
rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 18, 19, 20, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 167
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078028 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078028
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078028/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078028
Building REAL300000078029
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078029'
/scratch/stefan/7769659/working/building/REAL300000078029 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078029

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078029/0 /scratch/stefan/7769659/working/building/REAL300000078029 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/38
`/scratch/stefan/7769659/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NN(C)C=C1)

`REAL300000078029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078029 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.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', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 96, 133, 201, 201, 201, 96, 96, 96, 96, 96, 96, 96, 96, 96, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 96, 96, 96, 34, 35, 2, 2, 2, 1, 1] 201
rigid atoms, others: [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, 36, 37])
total number of confs: 679
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078029 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.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', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 13, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 46, 47, 96, 96, 96, 96, 96, 4, 4, 4, 13, 13, 1, 1, 1, 7, 7, 96, 96, 96, 96, 96] 201
rigid atoms, others: [32, 1, 6, 7, 8, 9, 10, 14, 15, 16, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 232
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078029 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078029/1 /scratch/stefan/7769659/working/building/REAL300000078029 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/39
`/scratch/stefan/7769659/working/3D/39' -> `1.mol2'
Preparing input files

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

`REAL300000078029.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078029/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078029 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 30, 30, 30, 21, 21, 18, 21, 21, 21, 21, 21, 21, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 30, 30, 21, 21, 21, 18, 5, 2, 2, 2, 1, 1] 30
rigid atoms, others: [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, 36, 37])
total number of confs: 103
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078029 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 12, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 17, 21, 21, 21, 21, 21, 4, 4, 4, 12, 12, 1, 1, 1, 4, 17, 21, 21, 21, 21, 21] 30
rigid atoms, others: [32, 1, 6, 7, 8, 9, 10, 14, 15, 16, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 96
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078029 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078029
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078029/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078029/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078029
Building REAL300000078030
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078030'
/scratch/stefan/7769659/working/building/REAL300000078030 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078030

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078030/0 /scratch/stefan/7769659/working/building/REAL300000078030 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/40
`/scratch/stefan/7769659/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-])

`REAL300000078030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078030 none COC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 39, 39, 39, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 137, 177, 177, 201, 185, 69, 69, 69, 39, 10, 10, 2, 2, 2, 1, 1, 39, 39, 177, 177, 177, 177] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 579
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078030 none COC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 36, 36, 39, 39, 39, 39, 39, 1, 1, 1, 1, 7, 13, 13, 25, 23, 3, 3, 3, 1, 8, 8, 39, 39, 39, 39, 39, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 35, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078030 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078030/1 /scratch/stefan/7769659/working/building/REAL300000078030 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/41
`/scratch/stefan/7769659/working/3D/41' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-])

`REAL300000078030.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078030/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078030 none COC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 28, 28, 28, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 110, 183, 190, 201, 190, 53, 53, 53, 28, 13, 4, 2, 2, 2, 1, 1, 28, 28, 183, 183, 190, 190] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 630
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078030 none COC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 21, 28, 28, 28, 28, 28, 1, 1, 1, 1, 9, 40, 50, 83, 71, 4, 4, 4, 1, 7, 21, 28, 28, 28, 28, 28, 1, 1, 40, 40, 50, 50] 201
rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 35, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 371
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078030 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078030
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078030/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078030/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078030
Building REAL300000078031
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078031'
/scratch/stefan/7769659/working/building/REAL300000078031 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078031

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078031/0 /scratch/stefan/7769659/working/building/REAL300000078031 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/42
`/scratch/stefan/7769659/working/3D/42' -> `0.mol2'
Preparing input files

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

`REAL300000078031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078031 none CC(=NNC1=NN(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 7, 20, 33, 54, 74, 74, 1, 11, 11, 11, 27, 27, 27, 27, 27, 27, 1, 1, 1, 20, 20, 33, 33, 54, 54, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 10, 11, 12, 13, 14, 15, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 377
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078031 none CC(=NNC1=NN(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 83, 124, 156, 201, 201, 201, 27, 6, 6, 6, 2, 2, 2, 2, 1, 1, 27, 27, 27, 124, 124, 156, 156, 201, 201, 27] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 733
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078031 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078031/1 /scratch/stefan/7769659/working/building/REAL300000078031 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/43
`/scratch/stefan/7769659/working/3D/43' -> `1.mol2'
Preparing input files

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

`REAL300000078031.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078031/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078031 none CC(N=NC1=NN(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 20, 20, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 7, 19, 23, 37, 50, 50, 1, 5, 5, 5, 5, 34, 34, 34, 34, 34, 1, 1, 1, 19, 19, 23, 23, 37, 37, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 10, 11, 12, 13, 14, 15, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 259
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078031 none CC(N=NC1=NN(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 34, 34, 119, 145, 150, 201, 201, 201, 34, 13, 13, 13, 13, 2, 2, 2, 1, 1, 34, 34, 34, 145, 145, 150, 150, 201, 201, 34] 201
rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 641
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078031 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078031
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078031/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078031/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078031
Building REAL300000078032
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078032'
/scratch/stefan/7769659/working/building/REAL300000078032 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078032

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078032/0 /scratch/stefan/7769659/working/building/REAL300000078032 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/44
`/scratch/stefan/7769659/working/3D/44' -> `0.mol2'
Preparing input files

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

`REAL300000078032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078032 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 24, 55, 62, 64, 64, 62, 62, 163, 199, 199, 201, 201, 64, 64, 6, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 60, 60, 61, 62, 64, 64, 199, 199, 199, 199, 64, 64, 2, 2, 2, 1, 1] 201
rigid atoms, others: [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, 40, 41, 42])
total number of confs: 630
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078032 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 4, 1, 1, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 1, 10, 39, 39, 64, 64, 64, 64, 64, 10, 10, 10, 10, 5, 5, 4, 4, 1, 1, 26, 26, 26, 26, 1, 1, 64, 64, 64, 64, 64] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 244
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078032 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078032
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078032/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078032
Building REAL300000078033
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078033'
/scratch/stefan/7769659/working/building/REAL300000078033 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078033

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078033/0 /scratch/stefan/7769659/working/building/REAL300000078033 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/45
`/scratch/stefan/7769659/working/3D/45' -> `0.mol2'
Preparing input files

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

`REAL300000078033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078033 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 21, 55, 60, 62, 62, 60, 60, 141, 201, 201, 201, 62, 62, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 57, 57, 58, 60, 62, 62, 201, 201, 62, 62, 2, 2, 2, 1, 1] 201
rigid atoms, others: [40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 676
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078033 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 4, 1, 1, 1, 1, 1, 1, 6, 24, 41, 41, 1, 1, 11, 40, 40, 62, 62, 62, 62, 62, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 24, 24, 1, 1, 62, 62, 62, 62, 62] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41])
total number of confs: 243
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078033 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078033
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078033/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078033
Building REAL300000078034
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078034'
/scratch/stefan/7769659/working/building/REAL300000078034 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078034

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078034/0 /scratch/stefan/7769659/working/building/REAL300000078034 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/46
`/scratch/stefan/7769659/working/3D/46' -> `0.mol2'
Preparing input files

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

`REAL300000078034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078034 none CC(N=NC1=NN(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 33, 33, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 11, 26, 26, 38, 38, 1, 8, 8, 8, 8, 52, 52, 52, 52, 52, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 214
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078034 none CC(N=NC1=NN(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 52, 52, 52, 52, 52, 154, 201, 201, 201, 201, 52, 16, 16, 16, 16, 2, 2, 2, 1, 1, 52, 52, 52, 201, 201, 201, 201, 52] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 511
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078034 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078034/1 /scratch/stefan/7769659/working/building/REAL300000078034 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/47
`/scratch/stefan/7769659/working/3D/47' -> `1.mol2'
Preparing input files

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

`REAL300000078034.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078034/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078034 none CC(=NNC1=NN(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 11, 28, 28, 44, 44, 1, 11, 11, 11, 41, 47, 47, 47, 47, 47, 1, 1, 1, 28, 28, 28, 28, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 259
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078034 none CC(=NNC1=NN(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 47, 47, 47, 141, 201, 201, 201, 201, 47, 11, 11, 11, 5, 2, 2, 2, 1, 1, 47, 47, 47, 201, 201, 201, 201, 47] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 531
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078034 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078034
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078034/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078034/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078034
Building REAL300000078035
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078035'
/scratch/stefan/7769659/working/building/REAL300000078035 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078035

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078035/0 /scratch/stefan/7769659/working/building/REAL300000078035 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/48
`/scratch/stefan/7769659/working/3D/48' -> `0.mol2'
Preparing input files

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

`REAL300000078035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078035 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 7, 26, 54, 62, 64, 64, 62, 62, 183, 201, 201, 201, 199, 64, 64, 7, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 58, 58, 60, 62, 64, 64, 201, 201, 201, 201, 64, 64, 2, 2, 2, 1, 1] 201
rigid atoms, others: [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, 40, 41, 42])
total number of confs: 528
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078035 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 4, 3, 1, 1, 1, 1, 1, 1, 6, 20, 20, 30, 27, 1, 1, 11, 37, 37, 64, 64, 64, 64, 64, 11, 11, 11, 11, 4, 4, 3, 3, 1, 1, 20, 20, 20, 20, 1, 1, 64, 64, 64, 64, 64] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 217
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078035 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078035
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078035/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078035
Building REAL300000078036
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078036'
/scratch/stefan/7769659/working/building/REAL300000078036 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078036

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078036/0 /scratch/stefan/7769659/working/building/REAL300000078036 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/49
`/scratch/stefan/7769659/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NN(C)C=C1)

`REAL300000078036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078036 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 18, 8, 8, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 65, 143, 143, 201, 201, 201, 201, 201, 65, 65, 65, 65, 22, 22, 18, 18, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201] 201
rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 18, 41, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078036 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 2, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 16, 1, 1, 8, 22, 22, 34, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 1, 1, 34, 34, 34, 34, 34] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 45, 46, 19, 20, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078036 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=NN(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 19, 32, 33, 34, 34, 33, 33, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 32, 32, 33, 33, 34, 34, 61, 61, 201, 201, 201, 201, 34, 34, 2, 2, 2, 1, 1] 201
rigid atoms, others: [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, 47, 48, 49])
total number of confs: 378
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078036 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078036
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078036/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078036
Building REAL300000078037
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078037'
/scratch/stefan/7769659/working/building/REAL300000078037 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078037

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078037/0 /scratch/stefan/7769659/working/building/REAL300000078037 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/50
`/scratch/stefan/7769659/working/3D/50' -> `0.mol2'
Preparing input files

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

`REAL300000078037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078037 none CCC(N=NC1=NN(C)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 1, 4, 11, 11, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 10, 26, 35, 58, 65, 68, 1, 1, 5, 5, 5, 5, 5, 4, 20, 20, 20, 20, 20, 1, 1, 10, 10, 26, 26, 35, 35, 58, 58, 1, 1] 201
rigid atoms, others: [2, 36, 37, 11, 12, 13, 14, 15, 46, 23, 24, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 348
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078037 none CCC(N=NC1=NN(C)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 12, 12, 75, 89, 135, 150, 196, 200, 201, 20, 20, 15, 15, 15, 15, 15, 10, 2, 2, 2, 1, 1, 20, 20, 88, 89, 135, 135, 150, 150, 196, 196, 20, 20] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 824
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078037 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078037/1 /scratch/stefan/7769659/working/building/REAL300000078037 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/51
`/scratch/stefan/7769659/working/3D/51' -> `1.mol2'
Preparing input files

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

`REAL300000078037.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078037/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078037 none CCC(=NNC1=NN(C)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 7, 7, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 6, 10, 25, 31, 50, 54, 57, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 1, 1, 10, 10, 24, 24, 31, 31, 49, 49, 1, 1] 201
rigid atoms, others: [2, 36, 37, 11, 12, 13, 14, 15, 46, 23, 24, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 330
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078037 none CCC(=NNC1=NN(C)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 6, 6, 57, 89, 139, 149, 190, 189, 191, 24, 24, 10, 10, 10, 10, 10, 2, 2, 2, 2, 1, 1, 24, 24, 89, 89, 139, 139, 149, 149, 190, 190, 24, 24] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 855
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078037 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078037
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078037/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078037/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078037
Building REAL300000078038
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078038'
/scratch/stefan/7769659/working/building/REAL300000078038 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078038

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078038/0 /scratch/stefan/7769659/working/building/REAL300000078038 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/52
`/scratch/stefan/7769659/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-])

`REAL300000078038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078038 none COC1=CC(C(C)=NNC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 36, 36, 36, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 103, 163, 173, 201, 201, 201, 60, 60, 60, 36, 7, 7, 7, 2, 2, 2, 2, 1, 1, 36, 36, 163, 163, 173, 173, 201, 201] 201
rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 713
number of broken/clashed sets: 103
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078038 none COC1=CC(C(C)=NNC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 11, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 9, 23, 29, 41, 53, 53, 3, 3, 3, 1, 11, 11, 11, 36, 36, 36, 36, 36, 36, 1, 1, 23, 23, 29, 29, 41, 41] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 15, 16, 17, 18, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 316
number of broken/clashed sets: 103
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078038 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078038/1 /scratch/stefan/7769659/working/building/REAL300000078038 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/53
`/scratch/stefan/7769659/working/3D/53' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)N=NC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-])

`REAL300000078038.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078038/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078038 none COC1=CC(C(C)N=NC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [64, 38, 38, 38, 11, 4, 11, 4, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 116, 177, 183, 201, 201, 201, 64, 64, 64, 38, 11, 11, 11, 11, 2, 2, 2, 1, 1, 38, 38, 177, 177, 183, 183, 201, 201] 201
rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 669
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078038 none COC1=CC(C(C)N=NC2=NN(C)C=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 7, 7, 26, 26, 38, 38, 38, 38, 38, 1, 1, 1, 1, 7, 17, 19, 29, 35, 35, 3, 3, 3, 1, 7, 7, 7, 7, 38, 38, 38, 38, 38, 1, 1, 17, 17, 19, 19, 29, 29] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 15, 16, 17, 18, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078038 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078038
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078038/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078038/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078038
Building REAL300000078039
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078039'
/scratch/stefan/7769659/working/building/REAL300000078039 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078039

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078039/0 /scratch/stefan/7769659/working/building/REAL300000078039 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/54
`/scratch/stefan/7769659/working/3D/54' -> `0.mol2'
Preparing input files

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

`REAL300000078039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078039 none CC(N=NC1=NN(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 32, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 53, 53, 7, 7, 7, 7, 55, 55, 55, 55, 55, 1, 1, 1, 33, 33] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 264
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078039 none CC(N=NC1=NN(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 24, 55, 55, 55, 24, 55, 55, 55, 142, 201, 201, 201, 24, 24, 24, 24, 2, 2, 2, 1, 1, 55, 55, 55, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078039 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078039/1 /scratch/stefan/7769659/working/building/REAL300000078039 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/55
`/scratch/stefan/7769659/working/3D/55' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=NN(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078039.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078039/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078039 none CC(=NNC1=NN(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 45, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 83, 83, 9, 9, 9, 45, 74, 74, 74, 74, 74, 1, 1, 1, 43, 43] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 419
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078039 none CC(=NNC1=NN(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 23, 74, 74, 74, 44, 74, 74, 74, 168, 201, 201, 201, 23, 23, 23, 5, 2, 2, 2, 1, 1, 74, 74, 74, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 543
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078039 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078039
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078039/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078039/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078039
Building REAL300000078040
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078040'
/scratch/stefan/7769659/working/building/REAL300000078040 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078040

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078040/0 /scratch/stefan/7769659/working/building/REAL300000078040 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/56
`/scratch/stefan/7769659/working/3D/56' -> `0.mol2'
Preparing input files

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

`REAL300000078040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078040 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NN(C)C=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 28, 7, 28, 7, 1, 1, 1, 1, 1, 1, 1, 55, 55, 67, 67, 67, 55, 55, 55, 55, 55, 55, 28, 28, 28, 28, 2, 2, 2, 1, 1, 67, 67] 67
rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 204
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078040 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=NN(C)C=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 5, 5, 38, 38, 55, 55, 55, 55, 55, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 55, 55, 55, 55, 55, 3, 3] 67
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 27, 28, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078040 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078040
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078040/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078040
Building REAL300000078041
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078041'
/scratch/stefan/7769659/working/building/REAL300000078041 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078041

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078041/0 /scratch/stefan/7769659/working/building/REAL300000078041 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/57
`/scratch/stefan/7769659/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1)

`REAL300000078041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 30, 30, 26, 30, 30, 1, 37, 37, 37, 37, 37, 37, 6, 6, 1, 1, 1, 26, 30, 30, 26, 30, 30, 1] 201
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 153
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 10, 37, 37, 37, 37, 37, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 37, 1, 2, 2, 2, 1, 1, 10, 9, 37, 37, 37, 201, 201, 201, 201, 201, 201, 37] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 586
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(N=NCC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 200, 200, 111, 30, 30, 30, 30, 30, 6, 3, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 30, 201, 201, 201, 201, 201, 201, 111, 111, 30, 30, 30, 3, 1, 1, 1, 1, 1, 30] 201
rigid atoms, others: [37, 38, 39, 40, 41, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42])
total number of confs: 510
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078041 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078041/1 /scratch/stefan/7769659/working/building/REAL300000078041 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/58
`/scratch/stefan/7769659/working/3D/58' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1)

`REAL300000078041.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078041/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 35, 51, 51, 35, 49, 49, 35, 49, 49, 1, 30, 30, 30, 30, 30, 30, 23, 6, 1, 1, 1, 35, 49, 49, 35, 49, 49, 1] 201
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 310
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 15, 15, 30, 30, 30, 30, 30, 101, 197, 201, 201, 197, 201, 201, 197, 201, 201, 30, 1, 2, 2, 2, 1, 1, 5, 15, 30, 30, 30, 197, 201, 201, 197, 201, 201, 30] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 639
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078041 none CN1C=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 135, 135, 49, 49, 49, 49, 49, 11, 4, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 201, 199, 135, 49, 49, 49, 4, 1, 1, 1, 1, 1, 49] 201
rigid atoms, others: [37, 38, 39, 40, 41, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42])
total number of confs: 513
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078041 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078041
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078041/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078041/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078041
Building REAL300000078042
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078042'
/scratch/stefan/7769659/working/building/REAL300000078042 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078042

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078042/0 /scratch/stefan/7769659/working/building/REAL300000078042 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/59
`/scratch/stefan/7769659/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=NN(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000078042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078042 none COC1=CC(C=NNC2=NN(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [61, 39, 39, 39, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 73, 103, 103, 107, 107, 61, 61, 61, 39, 16, 5, 2, 2, 2, 1, 1, 39, 103, 103, 103, 103] 107
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 323
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078042 none COC1=CC(C=NNC2=NN(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 31, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 4, 4, 4, 1, 7, 31, 39, 39, 39, 39, 39, 1, 14, 14, 14, 14] 107
rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 167
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078042 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078042/1 /scratch/stefan/7769659/working/building/REAL300000078042 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/60
`/scratch/stefan/7769659/working/3D/60' -> `1.mol2'
Preparing input files

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

`REAL300000078042.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078042/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078042 none COC1=CC(CN=NC2=NN(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 107, 107, 107, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 183, 201, 201, 201, 201, 142, 142, 142, 107, 21, 22, 2, 2, 2, 1, 1, 107, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 465
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078042 none COC1=CC(CN=NC2=NN(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 63, 64, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 5, 10, 10, 12, 12, 3, 3, 3, 1, 8, 8, 107, 107, 107, 107, 107, 1, 10, 10, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078042 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078042
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078042/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078042/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078042
Building REAL300000078043
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078043'
/scratch/stefan/7769659/working/building/REAL300000078043 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078043

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078043/0 /scratch/stefan/7769659/working/building/REAL300000078043 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/61
`/scratch/stefan/7769659/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1)

`REAL300000078043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 121, 65, 65, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 121, 121, 121, 121, 121, 121, 9, 9, 1, 1, 10, 10, 20, 10] 402
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 6, 24, 121, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 1, 2, 2, 2, 1, 1, 23, 24, 121, 121, 201, 201, 402, 201] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 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])
total number of confs: 719
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 171, 171, 61, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 201, 201, 201, 201, 201, 201, 61, 61, 10, 10, 1, 1, 2, 1] 402
rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 408
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078043 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078043/1 /scratch/stefan/7769659/working/building/REAL300000078043 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/62
`/scratch/stefan/7769659/working/3D/62' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1)

`REAL300000078043.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078043/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 35, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 46, 46, 46, 46, 46, 46, 34, 6, 1, 1, 12, 12, 24, 12] 168
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 21, 21, 46, 46, 46, 46, 84, 84, 84, 84, 84, 84, 84, 84, 84, 46, 1, 2, 2, 2, 1, 1, 7, 21, 46, 46, 84, 84, 168, 84] 168
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 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])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078043 none CN1C=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 84, 71, 37, 37, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 84, 84, 84, 84, 84, 84, 71, 37, 12, 12, 1, 1, 2, 1] 168
rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 221
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078043 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078043
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078043/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078043/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078043
Building REAL300000078044
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078044'
/scratch/stefan/7769659/working/building/REAL300000078044 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078044

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078044/0 /scratch/stefan/7769659/working/building/REAL300000078044 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/63
`/scratch/stefan/7769659/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1)

`REAL300000078044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 49, 49, 36, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 49, 49, 49, 49, 49, 49, 36, 7, 1, 1, 12, 12, 12, 12] 101
rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 22, 22, 49, 49, 49, 49, 101, 101, 101, 101, 101, 101, 101, 101, 49, 1, 2, 2, 2, 1, 1, 7, 22, 49, 49, 101, 101, 101, 101] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 88, 45, 45, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 101, 101, 101, 101, 101, 101, 88, 45, 12, 12, 1, 1, 1, 1] 101
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 267
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078044 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078044/1 /scratch/stefan/7769659/working/building/REAL300000078044 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/64
`/scratch/stefan/7769659/working/3D/64' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1)

`REAL300000078044.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078044/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 94, 94, 94, 59, 58, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 93, 94, 94, 94, 94, 94, 8, 8, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 3, 3, 19, 94, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 1, 2, 2, 2, 1, 1, 18, 19, 94, 94, 201, 201, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078044 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 169, 169, 60, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 60, 60, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 413
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078044 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078044
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078044/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078044/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078044
Building REAL300000078045
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078045'
/scratch/stefan/7769659/working/building/REAL300000078045 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078045

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078045/0 /scratch/stefan/7769659/working/building/REAL300000078045 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/65
`/scratch/stefan/7769659/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=N1)

`REAL300000078045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078045 none CN1C=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1] 21
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078045 none CN1C=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1, 7, 19, 21, 21, 21, 21] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 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
/scratch/stefan/7769659/working/building/REAL300000078045 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078045
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078045/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078045
Building REAL300000078046
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078046'
/scratch/stefan/7769659/working/building/REAL300000078046 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078046

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078046/0 /scratch/stefan/7769659/working/building/REAL300000078046 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/66
`/scratch/stefan/7769659/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=N1)

`REAL300000078046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078046 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 20, 10, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 20, 10, 1, 1, 1] 21
rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078046 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1, 5, 16, 21, 21, 21] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078046 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078046
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078046/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078046
Building REAL300000078047
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078047'
/scratch/stefan/7769659/working/building/REAL300000078047 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078047

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078047/0 /scratch/stefan/7769659/working/building/REAL300000078047 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/67
`/scratch/stefan/7769659/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=N1)

`REAL300000078047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078047 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 8, 1, 1, 2] 20
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 25
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078047 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 1, 1, 2, 6, 10, 10, 20] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 43
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078047 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078047/1 /scratch/stefan/7769659/working/building/REAL300000078047 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/68
`/scratch/stefan/7769659/working/3D/68' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=N1)

`REAL300000078047.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078047/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078047 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1] 6
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078047 none CN1C=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 2, 6, 6, 6] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28])
total number of confs: 16
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078047 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078047
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078047/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078047/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078047
Building REAL300000078048
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078048'
/scratch/stefan/7769659/working/building/REAL300000078048 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078048

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078048/0 /scratch/stefan/7769659/working/building/REAL300000078048 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/69
`/scratch/stefan/7769659/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(C=NNC2=NN(C)C=C2)=C1OCC(=O)[O-])

`REAL300000078048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078048 none COC1=CC(Br)=CC(C=NNC2=NN(C)C=C2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [30, 17, 17, 17, 17, 17, 17, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 29, 37, 39, 39, 30, 30, 30, 17, 17, 11, 5, 2, 2, 2, 1, 1, 37, 37] 39
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 128
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078048 none COC1=CC(Br)=CC(C=NNC2=NN(C)C=C2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 4, 4, 14, 17, 17, 17, 17, 17, 1, 1, 2, 10, 19, 19, 4, 4, 4, 1, 1, 4, 14, 17, 17, 17, 17, 17, 10, 10] 39
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 112
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078048 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078048/1 /scratch/stefan/7769659/working/building/REAL300000078048 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/70
`/scratch/stefan/7769659/working/3D/70' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(CN=NC2=NN(C)C=C2)=C1OCC(=O)[O-])

`REAL300000078048.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078048/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078048 none COC1=CC(Br)=CC(CN=NC2=NN(C)C=C2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [127, 80, 80, 80, 80, 80, 80, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 80, 80, 127, 199, 201, 201, 127, 127, 127, 80, 80, 25, 26, 2, 2, 2, 1, 1, 199, 199] 201
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078048 none COC1=CC(Br)=CC(CN=NC2=NN(C)C=C2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 48, 48, 80, 80, 80, 80, 80, 1, 1, 3, 13, 26, 26, 4, 4, 4, 1, 1, 8, 8, 80, 80, 80, 80, 80, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078048 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078048
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078048/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078048/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078048
Building REAL300000078049
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078049'
/scratch/stefan/7769659/working/building/REAL300000078049 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078049

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078049/0 /scratch/stefan/7769659/working/building/REAL300000078049 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/71
`/scratch/stefan/7769659/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1)

`REAL300000078049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(N=NCC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 33, 33, 4, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 1, 1, 66, 66, 66, 66, 66, 66, 4, 4, 1, 1, 2, 2, 17, 17, 1, 1] 201
rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 22, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(N=NCC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 25, 66, 66, 25, 37, 112, 112, 201, 201, 201, 201, 201, 201, 201, 66, 66, 1, 2, 2, 2, 1, 1, 24, 25, 66, 66, 112, 112, 201, 201, 66, 66] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(N=NCC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 177, 177, 51, 17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 201, 51, 51, 17, 17, 9, 9, 1, 1, 17, 17] 201
rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 402
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078049 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078049/1 /scratch/stefan/7769659/working/building/REAL300000078049 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/72
`/scratch/stefan/7769659/working/3D/72' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1)

`REAL300000078049.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078049/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [47, 47, 47, 47, 25, 5, 5, 1, 1, 1, 1, 1, 1, 2, 13, 55, 55, 55, 55, 55, 55, 55, 1, 1, 47, 47, 47, 47, 47, 47, 24, 5, 1, 1, 13, 13, 55, 55, 1, 1] 150
rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 22, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 186
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 26, 26, 47, 47, 26, 28, 69, 103, 150, 150, 150, 150, 150, 150, 150, 47, 47, 1, 2, 2, 2, 1, 1, 6, 26, 47, 47, 103, 103, 150, 150, 47, 47] 150
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 414
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078049 none CN1C=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [150, 150, 150, 150, 133, 105, 105, 55, 30, 55, 55, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 150, 150, 150, 150, 150, 150, 133, 105, 55, 55, 9, 9, 1, 1, 55, 55] 150
rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 515
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078049 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078049
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078049/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078049/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078049
Building REAL300000078050
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078050'
/scratch/stefan/7769659/working/building/REAL300000078050 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078050

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078050/0 /scratch/stefan/7769659/working/building/REAL300000078050 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/73
`/scratch/stefan/7769659/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=N1)

`REAL300000078050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078050 none CN1C=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 9, 7, 1, 1, 1] 14
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078050 none CN1C=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 1, 1, 5, 11, 14, 14, 14] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078050 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078050
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078050/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078050
Building REAL300000078051
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078051'
/scratch/stefan/7769659/working/building/REAL300000078051 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078051

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078051/0 /scratch/stefan/7769659/working/building/REAL300000078051 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/74
`/scratch/stefan/7769659/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=N1)

`REAL300000078051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078051 none CN1C=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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]
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, 15, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 15, 7, 2, 1, 1, 1, 1, 1] 34
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078051 none CN1C=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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]
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: [1, 1, 1, 1, 1, 1, 5, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 5, 10, 34, 17, 17, 17, 17, 17] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078051 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078051
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078051/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078051
Building REAL300000078052
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078052'
/scratch/stefan/7769659/working/building/REAL300000078052 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078052

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078052/0 /scratch/stefan/7769659/working/building/REAL300000078052 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/75
`/scratch/stefan/7769659/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1)

`REAL300000078052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 55, 55, 32, 32, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 13, 13, 5, 1, 1, 55, 55, 55, 55, 55, 55, 5, 5, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 21, 55, 55, 21, 21, 165, 165, 165, 165, 165, 201, 201, 201, 165, 55, 55, 1, 2, 2, 2, 1, 1, 20, 21, 55, 55, 165, 165, 165, 201, 201, 165, 55, 55] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 572
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(N=NCC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 165, 165, 165, 103, 103, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 5, 5, 165, 165, 165, 165, 165, 165, 17, 17, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201
rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41])
total number of confs: 305
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078052 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078052/1 /scratch/stefan/7769659/working/building/REAL300000078052 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/76
`/scratch/stefan/7769659/working/3D/76' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1)

`REAL300000078052.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078052/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 12, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 19, 19, 5, 1, 1, 18, 18, 18, 18, 18, 18, 12, 6, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 77
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 13, 18, 18, 14, 18, 45, 45, 45, 45, 45, 77, 77, 77, 45, 18, 18, 1, 2, 2, 2, 1, 1, 5, 13, 18, 18, 45, 45, 45, 77, 77, 45, 18, 18] 77
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078052 none CN1C=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 31, 17, 17, 3, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 45, 45, 45, 45, 45, 45, 31, 17, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 77
rigid atoms, others: [34, 35, 36, 39, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41])
total number of confs: 135
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078052 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078052
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078052/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078052/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078052
Building REAL300000078053
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078053'
/scratch/stefan/7769659/working/building/REAL300000078053 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078053

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078053/0 /scratch/stefan/7769659/working/building/REAL300000078053 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/77
`/scratch/stefan/7769659/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCC(=O)[O-])

`REAL300000078053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078053 none CCOC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 63, 33, 33, 33, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 137, 199, 199, 199, 65, 65, 65, 65, 65, 33, 8, 8, 2, 2, 2, 1, 1, 33, 33, 199, 199] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 617
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078053 none CCOC1=CC(CN=NC2=NN(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 6, 32, 32, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 23, 30, 30, 7, 7, 7, 7, 7, 1, 6, 6, 33, 33, 33, 33, 33, 1, 1, 23, 23] 201
rigid atoms, others: [2, 3, 4, 5, 6, 15, 16, 17, 18, 36, 28, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078053 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078053/1 /scratch/stefan/7769659/working/building/REAL300000078053 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/78
`/scratch/stefan/7769659/working/3D/78' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCC(=O)[O-])

`REAL300000078053.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078053/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078053 none CCOC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 53, 15, 15, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 76, 157, 177, 177, 91, 91, 91, 91, 91, 15, 4, 2, 2, 2, 2, 1, 1, 15, 15, 157, 157] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078053 none CCOC1=CC(C=NNC2=NN(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 9, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 40, 77, 77, 32, 32, 32, 32, 32, 1, 7, 15, 15, 15, 15, 15, 15, 1, 1, 41, 41] 201
rigid atoms, others: [2, 3, 4, 5, 6, 15, 16, 17, 18, 36, 28, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078053 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078053
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078053/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078053/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078053
Building REAL300000078054
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078054'
/scratch/stefan/7769659/working/building/REAL300000078054 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078054

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078054/0 /scratch/stefan/7769659/working/building/REAL300000078054 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/79
`/scratch/stefan/7769659/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])=N1)

`REAL300000078054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078054 none CN1C=CC(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 17, 17, 17, 16, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 16, 4, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 48
rigid atoms, others: [7, 8, 9, 10, 11, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078054 none CN1C=CC(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 13, 13, 17, 17, 17, 48, 48, 48, 48, 48, 17, 17, 17, 20, 20, 1, 2, 2, 2, 1, 1, 5, 13, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078054 none CN1C=CC(NN=CC2=CN(C3CCOCC3)N=C2C(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 44, 27, 27, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 17, 17, 48, 48, 48, 48, 48, 48, 44, 27, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 48
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 130
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078054 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078054
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078054/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078054
Building REAL300000078055
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078055'
/scratch/stefan/7769659/working/building/REAL300000078055 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078055

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078055/0 /scratch/stefan/7769659/working/building/REAL300000078055 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/80
`/scratch/stefan/7769659/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1)

`REAL300000078055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078055 none CN1C=CC(NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 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
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, 12, 4, 4, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 12, 4, 2, 2, 2, 1, 1, 1] 13
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 32, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078055 none CN1C=CC(NN=CC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 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
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, 5, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 1, 5, 11, 13, 13, 13, 13, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 28
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078055 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078055/1 /scratch/stefan/7769659/working/building/REAL300000078055 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/81
`/scratch/stefan/7769659/working/3D/81' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1)

`REAL300000078055.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078055/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078055 none CN1C=CC(N=NCC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 5, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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
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, 50, 49, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 86, 86, 86, 86, 86, 7, 7, 2, 2, 2, 1, 1, 1] 86
rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 32, 11, 12, 22, 23, 24, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078055 none CN1C=CC(N=NCC2=C(C(=O)[O-])N(C)C3=CC=C(F)C=C32)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 5, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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
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, 7, 7, 29, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 2, 2, 2, 1, 1, 28, 29, 86, 86, 86, 86, 86, 86] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078055 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078055
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078055/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078055/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078055
Building REAL300000078056
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078056'
/scratch/stefan/7769659/working/building/REAL300000078056 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078056

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078056/0 /scratch/stefan/7769659/working/building/REAL300000078056 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/82
`/scratch/stefan/7769659/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=C(C(=O)[O-])C=C(Br)S2)=N1)

`REAL300000078056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078056 none CN1C=CC(NN=CC2=C(C(=O)[O-])C=C(Br)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 15, 16, 12, 4, 4, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 12, 4, 1] 16
rigid atoms, others: [7, 8, 9, 10, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078056 none CN1C=CC(NN=CC2=C(C(=O)[O-])C=C(Br)S2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 1, 1, 4, 12, 16] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078056 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078056
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078056/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078056
Building REAL300000078057
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078057'
/scratch/stefan/7769659/working/building/REAL300000078057 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078057

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078057/0 /scratch/stefan/7769659/working/building/REAL300000078057 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/83
`/scratch/stefan/7769659/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1)

`REAL300000078057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(N=NCC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [37, 37, 37, 37, 31, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 63, 63, 63, 63, 63, 63, 63, 37, 37, 37, 37, 37, 37, 7, 7, 1, 1, 1, 1, 27, 27, 63, 63] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(N=NCC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 16, 37, 37, 37, 37, 37, 37, 90, 160, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 15, 16, 37, 37, 37, 37, 160, 160, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 577
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(N=NCC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 120, 63, 63, 63, 28, 63, 63, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 120, 120, 63, 28, 63, 63, 6, 6, 1, 1] 201
rigid atoms, others: [38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 568
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078057 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078057/1 /scratch/stefan/7769659/working/building/REAL300000078057 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/84
`/scratch/stefan/7769659/working/3D/84' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1)

`REAL300000078057.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078057/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 140, 140, 140, 140, 140, 140, 140, 19, 19, 19, 19, 19, 19, 14, 4, 1, 1, 1, 1, 36, 36, 140, 140] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 13, 13, 19, 19, 19, 19, 19, 19, 47, 120, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 5, 13, 19, 19, 19, 19, 120, 120, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078057 none CN1C=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 199, 186, 186, 140, 140, 140, 140, 140, 140, 59, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 199, 186, 140, 140, 140, 140, 9, 9, 1, 1] 201
rigid atoms, others: [38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 437
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078057 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078057
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078057/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078057/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078057
Building REAL300000078058
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078058'
/scratch/stefan/7769659/working/building/REAL300000078058 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078058

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078058/0 /scratch/stefan/7769659/working/building/REAL300000078058 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/85
`/scratch/stefan/7769659/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=CC(Br)=C2C(=O)[O-])=N1)

`REAL300000078058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078058 none CN1C=CC(NN=CC2=CC=CC(Br)=C2C(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 12, 9, 4, 1, 1, 1] 12
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078058 none CN1C=CC(NN=CC2=CC=CC(Br)=C2C(=O)[O-])=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 1, 1, 8, 12, 12, 12, 12] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28])
total number of confs: 28
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078058 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078058
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078058/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078058
Building REAL300000078059
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078059'
/scratch/stefan/7769659/working/building/REAL300000078059 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078059

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078059/0 /scratch/stefan/7769659/working/building/REAL300000078059 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/86
`/scratch/stefan/7769659/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1)

`REAL300000078059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078059 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 44, 10, 10, 1, 1, 1, 1, 1, 1, 9, 39, 62, 62, 1, 1, 1, 74, 74, 74, 74, 74, 74, 44, 10, 1, 1, 39, 39, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078059 none CN1C=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 27, 27, 74, 74, 46, 74, 148, 201, 201, 201, 74, 74, 74, 1, 2, 2, 2, 1, 1, 5, 27, 74, 74, 201, 201, 74] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078059 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078059/1 /scratch/stefan/7769659/working/building/REAL300000078059 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/87
`/scratch/stefan/7769659/working/3D/87' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1)

`REAL300000078059.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078059/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078059 none CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.2', '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, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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: [79, 79, 79, 79, 51, 51, 8, 1, 1, 1, 1, 1, 1, 7, 21, 26, 26, 1, 1, 1, 79, 79, 79, 79, 79, 79, 8, 8, 1, 1, 21, 21, 1] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078059 none CN1C=CC(N=NCC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'N.2', '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, 1, 12, 5, 1, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 18, 79, 79, 79, 79, 177, 201, 201, 201, 79, 79, 79, 1, 2, 2, 2, 1, 1, 17, 18, 79, 79, 201, 201, 79] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078059 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078059
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078059/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078059/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078059
Building REAL300000078060
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078060'
/scratch/stefan/7769659/working/building/REAL300000078060 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078060

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078060/0 /scratch/stefan/7769659/working/building/REAL300000078060 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/88
`/scratch/stefan/7769659/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1)

`REAL300000078060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078060 none CN1C=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 1, 1, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 9, 15, 15, 1, 1] 27
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078060 none CN1C=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 2, 4, 4, 8, 8, 4, 4, 13, 13, 13, 25, 27, 27, 27, 8, 8, 1, 2, 2, 2, 1, 1, 2, 4, 8, 8, 25, 27, 27, 8, 8] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078060 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078060/1 /scratch/stefan/7769659/working/building/REAL300000078060 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/89
`/scratch/stefan/7769659/working/3D/89' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(N=NCC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1)

`REAL300000078060.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078060/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078060 none CN1C=CC(N=NCC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 33, 33, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 1, 1, 67, 67, 67, 67, 67, 67, 5, 5, 1, 1, 9, 13, 13, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078060 none CN1C=CC(N=NCC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 5, 5, 29, 67, 67, 37, 67, 115, 115, 115, 201, 201, 201, 201, 67, 67, 1, 2, 2, 2, 1, 1, 28, 29, 67, 67, 201, 201, 201, 67, 67] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 876
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078060 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078060
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078060/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078060/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078060
Building REAL300000078061
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078061'
/scratch/stefan/7769659/working/building/REAL300000078061 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078061

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078061/0 /scratch/stefan/7769659/working/building/REAL300000078061 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/90
`/scratch/stefan/7769659/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=N1)

`REAL300000078061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078061 none CN1C=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 17, 11, 1, 1, 1] 25
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078061 none CN1C=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 1, 1, 5, 19, 25, 25, 25] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078061 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078061
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078061/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078061
Building REAL300000078062
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078062'
/scratch/stefan/7769659/working/building/REAL300000078062 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078062

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078062/0 /scratch/stefan/7769659/working/building/REAL300000078062 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/91
`/scratch/stefan/7769659/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)

`REAL300000078062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078062 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 33, 8, 8, 1, 1, 1, 101, 101] 101
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078062 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 7, 7, 29, 63, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 7, 29, 63, 63, 101, 101, 101, 1, 1] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078062 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078062
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078062/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078062
Building REAL300000078063
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078063'
/scratch/stefan/7769659/working/building/REAL300000078063 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078063

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078063/0 /scratch/stefan/7769659/working/building/REAL300000078063 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/92
`/scratch/stefan/7769659/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078063 none O=C([O-])COC1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 147, 72, 72, 72, 52, 72, 72, 52, 52, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 72, 72, 72, 72, 52, 31, 6, 6, 1, 1, 1] 201
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])
total number of confs: 654
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078063 none O=C([O-])COC1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 32, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 35, 72, 72, 72, 72, 72, 72, 72, 32, 32, 1, 1, 1, 1, 4, 6, 35, 35, 72, 72, 72] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078063 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078063
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078063/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078063
Building REAL300000078064
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078064'
/scratch/stefan/7769659/working/building/REAL300000078064 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078064

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078064/0 /scratch/stefan/7769659/working/building/REAL300000078064 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/93
`/scratch/stefan/7769659/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)

`REAL300000078064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078064 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 130, 70, 40, 82, 82, 40, 40, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 82, 82, 40, 23, 6, 6, 1, 1, 1, 82, 82] 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])
total number of confs: 798
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078064 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 11, 19, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 59, 82, 82, 82, 82, 82, 82, 82, 1, 1, 11, 11, 1, 1, 6, 15, 59, 59, 82, 82, 82, 1, 1] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 312
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078064 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078064
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078064/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078064
Building REAL300000078065
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078065'
/scratch/stefan/7769659/working/building/REAL300000078065 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078065

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078065/0 /scratch/stefan/7769659/working/building/REAL300000078065 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/94
`/scratch/stefan/7769659/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078065 none O=C([O-])C1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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
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, 19, 19, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 19, 17, 6, 6, 1, 1, 1] 20
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])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078065 none O=C([O-])C1=CC=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 4, 10, 17, 17, 20, 20, 20] 20
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 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
/scratch/stefan/7769659/working/building/REAL300000078065 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078065
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078065/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078065
Building REAL300000078066
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078066'
/scratch/stefan/7769659/working/building/REAL300000078066 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078066

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078066/0 /scratch/stefan/7769659/working/building/REAL300000078066 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/95
`/scratch/stefan/7769659/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC(Cl)=C1Cl)CCC2)

`REAL300000078066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078066 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC(Cl)=C1Cl)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 37, 8, 8, 1, 1, 1, 126, 126, 126, 126, 126, 126] 126
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, 35, 36, 37, 38])
total number of confs: 215
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078066 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC(Cl)=C1Cl)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 54, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 2, 2, 2, 8, 54, 54, 126, 126, 126, 1, 1, 1, 1, 1, 1] 126
rigid atoms, others: [0, 1, 2, 3, 36, 33, 6, 7, 8, 9, 10, 11, 34, 35, 21, 22, 23, 38, 37] set([32, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 299
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078066 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078066
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078066/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078066
Building REAL300000078067
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078067'
/scratch/stefan/7769659/working/building/REAL300000078067 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078067

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078067/0 /scratch/stefan/7769659/working/building/REAL300000078067 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/96
`/scratch/stefan/7769659/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)C(=O)[O-])

`REAL300000078067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078067 none CC(OC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 161, 64, 64, 64, 64, 64, 44, 44, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 44, 24, 6, 6, 1, 1, 1, 64] 201
rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 488
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078067 none CC(OC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
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, 1, 1, 1, 1, 4, 4, 9, 43, 64, 64, 63, 64, 64, 64, 64, 1, 23, 29, 29, 23, 23, 23, 23, 1, 1, 1, 4, 9, 44, 44, 64, 64, 63, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 38, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 273
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078067 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078067
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078067/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078067
Building REAL300000078068
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078068'
/scratch/stefan/7769659/working/building/REAL300000078068 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078068

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078068/0 /scratch/stefan/7769659/working/building/REAL300000078068 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/97
`/scratch/stefan/7769659/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078068 none O=C([O-])CCOC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 201, 167, 64, 64, 64, 64, 64, 34, 34, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 64, 64, 64, 34, 17, 5, 5, 1, 1, 1, 64] 201
rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 437
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078068 none O=C([O-])CCOC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 23, 17, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 50, 64, 64, 64, 64, 64, 64, 64, 1, 17, 17, 17, 17, 1, 1, 1, 6, 10, 50, 51, 64, 64, 64, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 38, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 287
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078068 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078068
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078068/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078068
Building REAL300000078069
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078069'
/scratch/stefan/7769659/working/building/REAL300000078069 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078069

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078069/0 /scratch/stefan/7769659/working/building/REAL300000078069 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/98
`/scratch/stefan/7769659/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1[N+](=O)[O-])

`REAL300000078069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078069 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 149, 49, 49, 78, 78, 33, 33, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 201, 201, 78, 78, 33, 17, 5, 5, 1, 1, 1, 78] 201
rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 647
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078069 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 21, 27, 7, 1, 1, 1, 1, 1, 1, 7, 7, 15, 65, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 2, 2, 21, 21, 1, 1, 7, 15, 65, 65, 78, 78, 78, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078069 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078069
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078069/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078069
Building REAL300000078070
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078070'
/scratch/stefan/7769659/working/building/REAL300000078070 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078070

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078070/0 /scratch/stefan/7769659/working/building/REAL300000078070 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/99
`/scratch/stefan/7769659/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078070 none O=C([O-])COC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 136, 52, 52, 52, 52, 52, 35, 35, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 52, 52, 52, 35, 25, 6, 6, 1, 1, 1, 52] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 576
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078070 none O=C([O-])COC1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 18, 27, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 36, 52, 52, 52, 52, 52, 52, 52, 1, 18, 18, 1, 1, 1, 4, 10, 36, 36, 52, 52, 52, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 22, 25, 26, 27] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078070 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078070
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078070/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078070
Building REAL300000078071
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078071'
/scratch/stefan/7769659/working/building/REAL300000078071 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078071

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078071/0 /scratch/stefan/7769659/working/building/REAL300000078071 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/100
`/scratch/stefan/7769659/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(OCC(=O)[O-])=C1)

`REAL300000078071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078071 none COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 82, 69, 82, 82, 69, 69, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 141, 201, 201, 201, 82, 86, 86, 86, 82, 82, 69, 33, 6, 6, 1, 1, 1, 201, 201, 82] 201
rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 652
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078071 none COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 41, 82, 82, 82, 82, 82, 82, 82, 1, 1, 7, 32, 44, 44, 1, 2, 2, 2, 1, 1, 4, 8, 41, 41, 82, 82, 82, 32, 32, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 18, 19, 24, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078071 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078071
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078071/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078071
Building REAL300000078072
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078072'
/scratch/stefan/7769659/working/building/REAL300000078072 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078072

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078072/0 /scratch/stefan/7769659/working/building/REAL300000078072 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/101
`/scratch/stefan/7769659/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)

`REAL300000078072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078072 none O=C([O-])C(F)(F)OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 118, 201, 201, 48, 42, 48, 48, 24, 24, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 24, 15, 5, 5, 1, 1, 1, 48, 48] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 639
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078072 none O=C([O-])C(F)(F)OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 32, 7, 23, 23, 1, 1, 1, 1, 1, 1, 6, 6, 13, 38, 48, 48, 47, 48, 48, 48, 48, 1, 1, 1, 1, 6, 12, 38, 38, 48, 48, 48, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078072 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078072
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078072/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078072
Building REAL300000078073
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078073'
/scratch/stefan/7769659/working/building/REAL300000078073 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078073

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078073/0 /scratch/stefan/7769659/working/building/REAL300000078073 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/102
`/scratch/stefan/7769659/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)

`REAL300000078073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078073 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 136, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 136, 35, 7, 7, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 344
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078073 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 35, 106, 201, 201, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 8, 35, 106, 106, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 24, 25, 38, 29, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 522
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078073 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078073
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078073/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078073
Building REAL300000078074
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078074'
/scratch/stefan/7769659/working/building/REAL300000078074 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078074

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078074/0 /scratch/stefan/7769659/working/building/REAL300000078074 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/103
`/scratch/stefan/7769659/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNCC3=CC=CC(Cl)=C3Cl)=C2C=C1)

`REAL300000078074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078074 none O=C([O-])C1=CC2=NNC(C=NNCC3=CC=CC(Cl)=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 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
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, 185, 185, 135, 135, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 135, 34, 8, 8, 1, 1, 1, 185, 185] 185
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: 308
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078074 none O=C([O-])C1=CC2=NNC(C=NNCC3=CC=CC(Cl)=C3Cl)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 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
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 38, 108, 185, 185, 185, 185, 185, 185, 185, 1, 1, 1, 1, 1, 8, 38, 108, 108, 185, 185, 185, 1, 1] 185
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 33] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 509
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078074 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078074/1 /scratch/stefan/7769659/working/building/REAL300000078074 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/104
`/scratch/stefan/7769659/working/3D/104' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=NNC2=C1)

`REAL300000078074.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078074/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078074 none O=C([O-])C1=CC=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 111, 34, 8, 8, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 342
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078074 none O=C([O-])C1=CC=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 120, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 45, 120, 120, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 550
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078074 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078074
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078074/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078074/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078074
Building REAL300000078075
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078075'
/scratch/stefan/7769659/working/building/REAL300000078075 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078075

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078075/0 /scratch/stefan/7769659/working/building/REAL300000078075 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/105
`/scratch/stefan/7769659/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N=N1)

`REAL300000078075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078075 none O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 116, 116, 116, 68, 68, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 116, 68, 25, 6, 6, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 638
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078075 none O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 12, 1, 1, 1, 1, 1, 6, 6, 28, 85, 116, 116, 116, 116, 116, 116, 116, 1, 1, 6, 6, 1, 6, 28, 85, 85, 116, 116, 116] 201
rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 382
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078075 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078075
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078075/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078075
Building REAL300000078076
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078076'
/scratch/stefan/7769659/working/building/REAL300000078076 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078076

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078076/0 /scratch/stefan/7769659/working/building/REAL300000078076 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/106
`/scratch/stefan/7769659/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCCC(=O)[O-])

`REAL300000078076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078076 none COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 61, 61, 61, 25, 25, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 137, 190, 190, 201, 195, 101, 101, 101, 61, 25, 15, 5, 5, 1, 1, 1, 61, 61, 190, 190, 190, 190] 201
rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 619
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078076 none COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 14, 51, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 7, 13, 14, 27, 25, 3, 3, 3, 1, 7, 14, 51, 51, 61, 61, 61, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 19, 20, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078076 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078076
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078076/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078076
Building REAL300000078077
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078077'
/scratch/stefan/7769659/working/building/REAL300000078077 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078077

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078077/0 /scratch/stefan/7769659/working/building/REAL300000078077 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/107
`/scratch/stefan/7769659/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(Cl)=C1)

`REAL300000078077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078077 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 151, 126, 151, 151, 126, 126, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 126, 41, 8, 8, 1, 1, 1, 151] 151
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 369
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078077 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47, 95, 151, 151, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 12, 47, 95, 95, 151, 151, 151, 1] 151
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 406
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078077 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078077
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078077/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078077
Building REAL300000078078
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078078'
/scratch/stefan/7769659/working/building/REAL300000078078 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078078

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078078/0 /scratch/stefan/7769659/working/building/REAL300000078078 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/108
`/scratch/stefan/7769659/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1O)

`REAL300000078078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078078 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
266  conformations in input
total number of sets (complete confs): 266
using faster count positions algorithm for large data
unique positions, atoms: [133, 133, 133, 133, 133, 81, 81, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 81, 35, 6, 6, 1, 1, 1, 133, 133, 266] 266
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078078 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
266  conformations in input
total number of sets (complete confs): 266
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 33, 87, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 9, 33, 87, 87, 133, 133, 133, 1, 1, 2] 266
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 30, 31] set([0, 32, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078078 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078078
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078078/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078078
Building REAL300000078079
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078079'
/scratch/stefan/7769659/working/building/REAL300000078079 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078079

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078079/0 /scratch/stefan/7769659/working/building/REAL300000078079 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/109
`/scratch/stefan/7769659/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-])

`REAL300000078079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078079 none CC(OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 77, 48, 106, 106, 48, 48, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 106, 106, 48, 28, 6, 6, 1, 1, 1, 106, 106] 201
rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 709
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078079 none CC(OC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 14, 72, 106, 106, 106, 106, 106, 106, 106, 1, 1, 14, 20, 20, 14, 14, 14, 14, 1, 1, 6, 14, 72, 72, 106, 106, 106, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 371
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078079 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078079
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078079/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078079
Building REAL300000078080
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078080'
/scratch/stefan/7769659/working/building/REAL300000078080 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078080

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078080/0 /scratch/stefan/7769659/working/building/REAL300000078080 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/110
`/scratch/stefan/7769659/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)C2=CC=CC=C21)

`REAL300000078080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078080 none O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 124, 124, 124, 60, 60, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 201, 201, 124, 60, 29, 6, 6, 1, 1, 1, 124, 124, 124, 124] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078080 none O=C([O-])CN1C=C(C=NNCC2=CC=CC(Cl)=C2Cl)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 12, 1, 1, 1, 1, 1, 6, 6, 23, 81, 124, 124, 123, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 22, 81, 81, 124, 124, 123, 1, 1, 1, 1] 201
rigid atoms, others: [35, 3, 4, 5, 6, 7, 38, 19, 20, 21, 22, 23, 24, 36, 27, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078080 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078080
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078080/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078080
Building REAL300000078081
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078081'
/scratch/stefan/7769659/working/building/REAL300000078081 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078081

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078081/0 /scratch/stefan/7769659/working/building/REAL300000078081 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/111
`/scratch/stefan/7769659/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N1)

`REAL300000078081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078081 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 155, 155, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 38, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 327
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078081 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC(Cl)=C2Cl)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 31, 110, 201, 201, 200, 201, 201, 201, 201, 1, 2, 2, 2, 1, 8, 31, 111, 111, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 20, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 531
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078081 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078081
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078081/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078081
Building REAL300000078082
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078082'
/scratch/stefan/7769659/working/building/REAL300000078082 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078082

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078082/0 /scratch/stefan/7769659/working/building/REAL300000078082 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/112
`/scratch/stefan/7769659/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078082 none O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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
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, 169, 169, 169, 169, 121, 121, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 121, 39, 8, 8, 1, 1, 1, 169] 169
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 295
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078082 none O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 97, 169, 169, 169, 169, 169, 169, 169, 1, 1, 1, 1, 9, 47, 97, 97, 169, 169, 169, 1] 169
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 431
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078082 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078082
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078082/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078082
Building REAL300000078083
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078083'
/scratch/stefan/7769659/working/building/REAL300000078083 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078083

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078083/0 /scratch/stefan/7769659/working/building/REAL300000078083 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/113
`/scratch/stefan/7769659/working/3D/113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000078083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078083 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 15, 34, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 6, 14, 14, 21, 30, 30, 1, 9, 9, 9, 15, 34, 34, 40, 40, 40, 1, 1, 1, 14, 14, 14, 14, 21, 21, 1] 201
rigid atoms, others: [1, 35, 36, 37, 44, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 243
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078083 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 40, 40, 111, 141, 141, 201, 201, 201, 40, 13, 13, 13, 11, 3, 3, 1, 1, 1, 40, 40, 40, 141, 141, 141, 141, 201, 201, 40] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 689
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078083 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078083
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078083/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078083
Building REAL300000078084
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078084'
/scratch/stefan/7769659/working/building/REAL300000078084 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078084

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078084/0 /scratch/stefan/7769659/working/building/REAL300000078084 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/114
`/scratch/stefan/7769659/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC(Cl)=C1Cl)

`REAL300000078084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078084 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 66, 76, 76, 76, 76, 76, 76, 182, 201, 201, 201, 76, 76, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 76, 76, 76, 76, 76, 76, 201, 201, 76, 76, 6, 6, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078084 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 23, 23, 1, 1, 3, 10, 10, 38, 76, 76, 76, 76, 76, 76, 76, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 12, 12, 1, 1, 38, 38, 76, 76, 76] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078084 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078084
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078084/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078084
Building REAL300000078085
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078085'
/scratch/stefan/7769659/working/building/REAL300000078085 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078085

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078085/0 /scratch/stefan/7769659/working/building/REAL300000078085 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/115
`/scratch/stefan/7769659/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000078085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078085 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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: [8, 1, 8, 8, 13, 54, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 11, 22, 22, 30, 30, 1, 8, 8, 8, 13, 54, 54, 78, 78, 78, 1, 1, 1, 22, 22, 22, 22, 1] 201
rigid atoms, others: [1, 34, 35, 36, 41, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 322
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078085 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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: [36, 36, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 78, 78, 78, 78, 78, 170, 201, 201, 201, 201, 78, 36, 36, 36, 19, 6, 6, 1, 1, 1, 78, 78, 78, 201, 201, 201, 201, 78] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 465
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078085 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078085
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078085/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078085
Building REAL300000078086
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078086'
/scratch/stefan/7769659/working/building/REAL300000078086 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078086

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078086/0 /scratch/stefan/7769659/working/building/REAL300000078086 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/116
`/scratch/stefan/7769659/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CSC(C(=O)[O-])=C1)

`REAL300000078086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078086 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 47, 121, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 47, 121, 121, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 560
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078086 none CC(=NNCC1=CC=CC(Cl)=C1Cl)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 39, 8, 8, 1, 1, 1, 201, 201] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 336
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078086 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078086
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078086/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078086
Building REAL300000078087
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078087'
/scratch/stefan/7769659/working/building/REAL300000078087 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078087

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078087/0 /scratch/stefan/7769659/working/building/REAL300000078087 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/117
`/scratch/stefan/7769659/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=CC(Cl)=C2Cl)C1)

`REAL300000078087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078087 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=CC(Cl)=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 88, 201, 201, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 5, 5, 22, 88, 88, 201, 201, 201, 5, 5] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 473
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078087 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=CC(Cl)=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 9, 53, 130, 130, 129, 130, 130, 130, 130, 1, 5, 5, 1, 5, 5, 1, 1, 9, 53, 53, 130, 130, 129, 1, 1] 201
rigid atoms, others: [1, 3, 4, 37, 38, 10, 11, 12, 13, 23, 29, 30] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 311
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078087 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNCC2=CC=CC(Cl)=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 130, 201, 130, 130, 201, 201, 130, 201, 201, 130, 130, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 130, 201, 201, 130, 130, 36, 6, 6, 1, 1, 1, 130, 130] 201
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 854
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078087 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078087
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078087/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078087
Building REAL300000078088
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078088'
/scratch/stefan/7769659/working/building/REAL300000078088 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078088

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078088/0 /scratch/stefan/7769659/working/building/REAL300000078088 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/118
`/scratch/stefan/7769659/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NCC1=CC=CC(Cl)=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000078088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078088 none CC(N=NCC1=CC=CC(Cl)=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 21, 21, 82, 154, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 82, 82, 154, 154, 154, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [1, 34, 35, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078088 none CC(N=NCC1=CC=CC(Cl)=C1Cl)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 43, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 154, 154, 154, 154, 154, 201, 201, 201, 154, 154, 154, 142, 142, 142, 142, 6, 6, 1, 1, 1, 154, 154, 201, 201, 154, 154, 154, 154, 154, 154] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 799
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078088 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078088
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078088/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078088
Building REAL300000078089
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078089'
/scratch/stefan/7769659/working/building/REAL300000078089 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078089

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078089/0 /scratch/stefan/7769659/working/building/REAL300000078089 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/119
`/scratch/stefan/7769659/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])N=NCC1=CC=CC(Cl)=C1Cl)

`REAL300000078089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078089 none CC(CCCCCCC(=O)[O-])N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 37, 80, 105, 105, 111, 133, 140, 201, 201, 201, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 105, 105, 105, 105, 111, 111, 133, 133, 140, 140, 201, 201, 6, 6, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 901
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078089 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078089
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078089/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078089
Building REAL300000078090
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078090'
/scratch/stefan/7769659/working/building/REAL300000078090 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078090

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078090/0 /scratch/stefan/7769659/working/building/REAL300000078090 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/120
`/scratch/stefan/7769659/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl)

`REAL300000078090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078090 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 139, 139, 201, 201, 201, 139, 139, 46, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 128, 139, 201, 201, 139, 139, 139, 139, 139, 6, 6, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 713
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078090 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 12, 12, 1, 1, 1, 1, 11, 11, 52, 139, 139, 139, 139, 139, 139, 139, 2, 2, 2, 1, 1, 6, 6, 1, 1, 1, 1, 1, 52, 52, 139, 139, 139] 201
rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 24, 25, 28, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 33, 34, 35, 36, 37])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078090 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078090
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078090/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078090
Building REAL300000078091
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078091'
/scratch/stefan/7769659/working/building/REAL300000078091 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078091

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078091/0 /scratch/stefan/7769659/working/building/REAL300000078091 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/121
`/scratch/stefan/7769659/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NCC2=CC=CC(Cl)=C2Cl)CCC(C(=O)[O-])C1(C)C)

`REAL300000078091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078091 none CC1C(N=NCC2=CC=CC(Cl)=C2Cl)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 56, 56, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 8, 8, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107] 107
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078091 none CC1C(N=NCC2=CC=CC(Cl)=C2Cl)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 10, 10, 59, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 107
rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40] set([32, 42, 43, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 41, 28, 29, 30, 31])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078091 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078091
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078091/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078091
Building REAL300000078092
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078092'
/scratch/stefan/7769659/working/building/REAL300000078092 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078092

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078092/0 /scratch/stefan/7769659/working/building/REAL300000078092 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/122
`/scratch/stefan/7769659/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl)

`REAL300000078092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078092 none CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 140, 140, 140, 140, 140, 140, 140, 140, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 8, 8, 1, 1, 1] 140
rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 334
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078092 none CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 10, 10, 54, 140, 140, 140, 140, 140, 140, 140, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 140, 140, 140] 140
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37])
total number of confs: 299
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078092 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078092
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078092/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078092
Building REAL300000078093
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078093'
/scratch/stefan/7769659/working/building/REAL300000078093 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078093

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078093/0 /scratch/stefan/7769659/working/building/REAL300000078093 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/123
`/scratch/stefan/7769659/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NCC2=CC=CC(Cl)=C2Cl)CCC1C(=O)[O-])

`REAL300000078093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078093 none CC1CC(N=NCC2=CC=CC(Cl)=C2Cl)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 45, 44, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 8, 8, 1, 1, 1, 70, 70, 70, 70, 70] 70
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37])
total number of confs: 161
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078093 none CC1CC(N=NCC2=CC=CC(Cl)=C2Cl)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 34, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 1, 34, 34, 70, 70, 70, 1, 1, 1, 1, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 37, 33, 34, 15, 16, 17, 18, 35, 24, 25, 26, 27, 36] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 172
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078093 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078093
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078093/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078093
Building REAL300000078094
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078094'
/scratch/stefan/7769659/working/building/REAL300000078094 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078094

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078094/0 /scratch/stefan/7769659/working/building/REAL300000078094 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/124
`/scratch/stefan/7769659/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CN1)

`REAL300000078094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078094 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 171, 171, 171, 110, 110, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 110, 33, 8, 8, 1, 1, 1, 171, 171] 171
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28, 29])
total number of confs: 306
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078094 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CN1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [2, 1, 2, 1, 1, 1, 1, 8, 8, 41, 94, 171, 171, 171, 171, 171, 171, 171, 1, 1, 1, 8, 41, 94, 94, 171, 171, 171, 1, 1] 171
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 430
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078094 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078094
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078094/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078094
Building REAL300000078095
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078095'
/scratch/stefan/7769659/working/building/REAL300000078095 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078095

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078095/0 /scratch/stefan/7769659/working/building/REAL300000078095 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/125
`/scratch/stefan/7769659/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC(Cl)=C1Cl)

`REAL300000078095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078095 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 45, 132, 173, 201, 201, 201, 201, 201, 201, 44, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 173, 173, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 769
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078095 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 1, 1, 3, 3, 1, 1, 1, 9, 34, 34, 124, 201, 201, 201, 201, 201, 201, 201, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 124, 124, 201, 201, 201] 201
rigid atoms, others: [32, 2, 3, 4, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37])
total number of confs: 548
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078095 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078095
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078095/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078095
Building REAL300000078096
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078096'
/scratch/stefan/7769659/working/building/REAL300000078096 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078096

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078096/0 /scratch/stefan/7769659/working/building/REAL300000078096 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/126
`/scratch/stefan/7769659/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078096 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 98, 98, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 141, 98, 33, 8, 8, 1, 1, 1] 141
rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 245
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078096 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 40, 88, 141, 141, 141, 141, 141, 141, 141, 2, 2, 2, 1, 2, 2, 2, 1, 10, 40, 88, 88, 141, 141, 141] 141
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078096 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078096
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078096/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078096
Building REAL300000078097
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078097'
/scratch/stefan/7769659/working/building/REAL300000078097 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078097

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078097/0 /scratch/stefan/7769659/working/building/REAL300000078097 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/127
`/scratch/stefan/7769659/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1Cl)

`REAL300000078097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078097 none O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 141, 141, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 38, 8, 8, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 337
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078097 none O=C([O-])C1=CC=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 46, 125, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 46, 125, 125, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 552
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078097 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078097
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078097/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078097
Building REAL300000078098
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078098'
/scratch/stefan/7769659/working/building/REAL300000078098 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078098

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078098/0 /scratch/stefan/7769659/working/building/REAL300000078098 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/128
`/scratch/stefan/7769659/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1F)

`REAL300000078098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078098 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 113, 113, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 113, 35, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 368
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078098 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 43, 109, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 8, 43, 109, 109, 201, 201, 201, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078098 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078098
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078098/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078098
Building REAL300000078099
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078099'
/scratch/stefan/7769659/working/building/REAL300000078099 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078099

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078099/0 /scratch/stefan/7769659/working/building/REAL300000078099 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/129
`/scratch/stefan/7769659/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1)

`REAL300000078099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078099 none O=C([O-])C=CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 141, 141, 141, 141, 107, 107, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 141, 141, 107, 33, 6, 6, 1, 1, 1] 201
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078099 none O=C([O-])C=CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 24, 10, 1, 1, 1, 1, 1, 1, 4, 4, 18, 81, 141, 141, 141, 141, 141, 141, 141, 1, 10, 10, 1, 1, 4, 18, 81, 81, 141, 141, 141] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 428
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078099 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078099
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078099/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078099
Building REAL300000078100
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078100'
/scratch/stefan/7769659/working/building/REAL300000078100 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078100

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078100/0 /scratch/stefan/7769659/working/building/REAL300000078100 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/130
`/scratch/stefan/7769659/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1)

`REAL300000078100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078100 none O=C([O-])C1=CC=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 143, 36, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 332
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078100 none O=C([O-])C1=CC=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 107, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 43, 107, 107, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 512
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078100 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078100
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078100/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078100
Building REAL300000078101
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078101'
/scratch/stefan/7769659/working/building/REAL300000078101 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078101

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078101/0 /scratch/stefan/7769659/working/building/REAL300000078101 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/131
`/scratch/stefan/7769659/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=N1)

`REAL300000078101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078101 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 111, 111, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 111, 35, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 375
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078101 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 50, 111, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 10, 50, 111, 111, 201, 201, 201, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 500
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078101 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078101
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078101/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078101
Building REAL300000078102
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078102'
/scratch/stefan/7769659/working/building/REAL300000078102 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078102

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078102/0 /scratch/stefan/7769659/working/building/REAL300000078102 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/132
`/scratch/stefan/7769659/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1O)

`REAL300000078102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078102 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 117, 117, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 117, 35, 8, 8, 1, 1, 1, 201, 402] 402
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 767
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078102 none O=C([O-])C1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 45, 106, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 8, 45, 106, 106, 201, 201, 201, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 31] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 501
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078102 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078102
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078102/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078102
Building REAL300000078103
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078103'
/scratch/stefan/7769659/working/building/REAL300000078103 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078103

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078103/0 /scratch/stefan/7769659/working/building/REAL300000078103 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/133
`/scratch/stefan/7769659/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1C(=O)[O-])

`REAL300000078103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078103 none CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [187, 187, 187, 187, 97, 97, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 187, 187, 187, 187, 97, 35, 6, 6, 1, 1, 1, 187] 187
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078103 none CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 10, 10, 43, 113, 187, 187, 187, 187, 187, 187, 187, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 10, 43, 113, 113, 187, 187, 187, 1] 187
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 505
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078103 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078103
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078103/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078103
Building REAL300000078104
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078104'
/scratch/stefan/7769659/working/building/REAL300000078104 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078104

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078104/0 /scratch/stefan/7769659/working/building/REAL300000078104 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/134
`/scratch/stefan/7769659/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078104 none O=C([O-])C1=C(Cl)SC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 126, 37, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 28])
total number of confs: 342
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078104 none O=C([O-])C1=C(Cl)SC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 38, 115, 201, 201, 201, 201, 201, 201, 201, 1, 7, 38, 115, 115, 201, 201, 201, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 525
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078104 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078104
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078104/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078104
Building REAL300000078105
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078105'
/scratch/stefan/7769659/working/building/REAL300000078105 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078105

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078105/0 /scratch/stefan/7769659/working/building/REAL300000078105 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/135
`/scratch/stefan/7769659/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078105 none O=C([O-])C1=CN=C(Cl)C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 14, 14, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 5, 5, 1, 1, 1] 14
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27])
total number of confs: 42
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078105 none O=C([O-])C1=CN=C(Cl)C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 4, 7, 14, 14, 14, 14, 14] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078105 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078105
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078105/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078105
Building REAL300000078106
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078106'
/scratch/stefan/7769659/working/building/REAL300000078106 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078106

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078106/0 /scratch/stefan/7769659/working/building/REAL300000078106 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/136
`/scratch/stefan/7769659/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078106 none CN1N=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 167, 115, 115, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 115, 37, 8, 8, 1, 1, 1] 167
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])
total number of confs: 306
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078106 none CN1N=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 117, 167, 167, 167, 167, 167, 167, 167, 2, 2, 2, 1, 9, 47, 117, 117, 167, 167, 167] 167
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 491
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078106 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078106
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078106/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078106
Building REAL300000078107
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078107'
/scratch/stefan/7769659/working/building/REAL300000078107 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078107

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078107/0 /scratch/stefan/7769659/working/building/REAL300000078107 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/137
`/scratch/stefan/7769659/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078107 none CN1C=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 164, 115, 115, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 115, 39, 8, 8, 1, 1, 1] 164
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078107 none CN1C=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 46, 111, 164, 164, 164, 164, 164, 164, 164, 2, 2, 2, 1, 1, 9, 46, 111, 111, 164, 164, 164] 164
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 24, 25] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 475
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078107 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078107
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078107/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078107
Building REAL300000078108
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078108'
/scratch/stefan/7769659/working/building/REAL300000078108 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078108

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078108/0 /scratch/stefan/7769659/working/building/REAL300000078108 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/138
`/scratch/stefan/7769659/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078108 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 102, 102, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 120, 120, 120, 102, 31, 8, 8, 1, 1, 1] 120
rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 212
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078108 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 32, 71, 120, 120, 120, 120, 120, 120, 120, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 32, 71, 71, 120, 120, 120] 120
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 313
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078108 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078108
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078108/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078108
Building REAL300000078109
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078109'
/scratch/stefan/7769659/working/building/REAL300000078109 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078109

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078109/0 /scratch/stefan/7769659/working/building/REAL300000078109 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/139
`/scratch/stefan/7769659/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNCC2=CC=CC(Cl)=C2Cl)S1)

`REAL300000078109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078109 none CCC1=CC(C(=O)[O-])=C(C=NNCC2=CC=CC(Cl)=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 67, 67, 67, 67, 67, 67, 67, 57, 57, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 111, 111, 111, 111, 111, 67, 57, 27, 6, 6, 1, 1, 1] 111
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 399
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078109 none CCC1=CC(C(=O)[O-])=C(C=NNCC2=CC=CC(Cl)=C2Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 13, 47, 67, 67, 67, 67, 67, 67, 67, 1, 6, 6, 6, 6, 6, 1, 3, 13, 47, 47, 67, 67, 67] 111
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 21, 27] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078109 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078109
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078109/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078109
Building REAL300000078110
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078110'
/scratch/stefan/7769659/working/building/REAL300000078110 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078110

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078110/0 /scratch/stefan/7769659/working/building/REAL300000078110 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/140
`/scratch/stefan/7769659/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078110 none COC1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 133, 37, 8, 8, 1, 1, 1] 201
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])
total number of confs: 338
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078110 none COC1=CC=C(C(=O)[O-])C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 104, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 6, 35, 104, 104, 201, 201, 201] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 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: 504
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078110 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078110
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078110/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078110
Building REAL300000078111
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078111'
/scratch/stefan/7769659/working/building/REAL300000078111 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078111

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078111/0 /scratch/stefan/7769659/working/building/REAL300000078111 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/141
`/scratch/stefan/7769659/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1)

`REAL300000078111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078111 none O=C([O-])C1=CC=C2SC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 142, 37, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 333
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078111 none O=C([O-])C1=CC=C2SC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 43, 107, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 43, 107, 107, 201, 201, 201, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 510
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078111 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078111
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078111/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078111
Building REAL300000078112
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078112'
/scratch/stefan/7769659/working/building/REAL300000078112 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078112

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078112/0 /scratch/stefan/7769659/working/building/REAL300000078112 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/142
`/scratch/stefan/7769659/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=COC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078112 none O=C([O-])C1=COC(C=NNCC2=CC=CC(Cl)=C2Cl)=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.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [189, 189, 189, 189, 189, 189, 113, 113, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 189, 189, 113, 35, 8, 8, 1, 1, 1, 189] 189
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 347
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078112 none O=C([O-])C1=COC(C=NNCC2=CC=CC(Cl)=C2Cl)=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.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 44, 99, 189, 189, 189, 189, 189, 189, 189, 1, 1, 8, 44, 99, 99, 189, 189, 189, 1] 189
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 454
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078112 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078112
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078112/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078112
Building REAL300000078113
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078113'
/scratch/stefan/7769659/working/building/REAL300000078113 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078113

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078113/0 /scratch/stefan/7769659/working/building/REAL300000078113 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/143
`/scratch/stefan/7769659/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(C(=O)[O-])=C1)

`REAL300000078113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078113 none CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 16, 6, 6, 1, 1, 1, 20] 20
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078113 none CC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 4, 10, 16, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 4, 10, 16, 16, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 18, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078113 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078113
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078113/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078113
Building REAL300000078114
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078114'
/scratch/stefan/7769659/working/building/REAL300000078114 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078114

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078114/0 /scratch/stefan/7769659/working/building/REAL300000078114 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/144
`/scratch/stefan/7769659/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1C(=O)[O-])

`REAL300000078114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078114 none COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 162, 162, 162, 70, 70, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 201, 201, 201, 162, 70, 33, 6, 6, 1, 1, 1, 162, 162] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 523
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078114 none COC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 28, 101, 162, 162, 162, 162, 162, 162, 162, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 28, 101, 101, 162, 162, 162, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078114 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078114
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078114/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078114
Building REAL300000078115
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078115'
/scratch/stefan/7769659/working/building/REAL300000078115 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078115

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078115/0 /scratch/stefan/7769659/working/building/REAL300000078115 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/145
`/scratch/stefan/7769659/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(F)=C1)

`REAL300000078115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078115 none O=C([O-])C1=CC(F)=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 113, 135, 135, 135, 113, 113, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 113, 39, 8, 8, 1, 1, 1, 135] 135
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 362
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078115 none O=C([O-])C1=CC(F)=C(C=NNCC2=CC=CC(Cl)=C2Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 49, 93, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1, 7, 49, 93, 93, 135, 135, 135, 1] 135
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 377
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078115 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078115
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078115/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078115
Building REAL300000078116
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078116'
/scratch/stefan/7769659/working/building/REAL300000078116 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078116

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078116/0 /scratch/stefan/7769659/working/building/REAL300000078116 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/146
`/scratch/stefan/7769659/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078116 none CC1=C(C(=O)[O-])NC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 126, 126, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 126, 37, 8, 8, 1, 1, 1, 175] 175
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 301
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078116 none CC1=C(C(=O)[O-])NC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 28, 87, 175, 175, 175, 175, 175, 175, 175, 1, 2, 2, 2, 1, 9, 28, 87, 87, 175, 175, 174, 1] 175
rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 20, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078116 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078116
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078116/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078116
Building REAL300000078117
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078117'
/scratch/stefan/7769659/working/building/REAL300000078117 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078117

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078117/0 /scratch/stefan/7769659/working/building/REAL300000078117 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/147
`/scratch/stefan/7769659/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1O)

`REAL300000078117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078117 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 104, 36, 7, 7, 1, 1, 1, 402] 402
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078117 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 104, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 34, 104, 104, 201, 201, 201, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 31])
total number of confs: 503
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078117 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078117
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078117/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078117
Building REAL300000078118
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078118'
/scratch/stefan/7769659/working/building/REAL300000078118 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078118

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078118/0 /scratch/stefan/7769659/working/building/REAL300000078118 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/148
`/scratch/stefan/7769659/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC(Cl)=C1)

`REAL300000078118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078118 none O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 43, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 43, 29, 6, 6, 1, 1, 1, 46] 46
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078118 none O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 3, 3, 11, 31, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 3, 11, 31, 31, 46, 46, 46, 1] 46
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078118 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078118
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078118/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078118
Building REAL300000078119
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078119'
/scratch/stefan/7769659/working/building/REAL300000078119 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078119

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078119/0 /scratch/stefan/7769659/working/building/REAL300000078119 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/149
`/scratch/stefan/7769659/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC=C1)

`REAL300000078119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078119 none O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 39, 39, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 39, 27, 6, 6, 1, 1, 1, 47, 47] 47
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078119 none O=C([O-])C1=C(C=NNCC2=CC=CC(Cl)=C2Cl)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 14, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 3, 3, 13, 29, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 13, 29, 29, 47, 47, 47, 1, 1] 47
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 27, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078119 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078119
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078119/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078119
Building REAL300000078120
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078120'
/scratch/stefan/7769659/working/building/REAL300000078120 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078120

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078120/0 /scratch/stefan/7769659/working/building/REAL300000078120 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/150
`/scratch/stefan/7769659/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CS1)

`REAL300000078120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078120 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [163, 163, 163, 163, 163, 118, 118, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 118, 38, 8, 8, 1, 1, 1, 163] 163
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 285
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078120 none O=C([O-])C1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 9, 9, 42, 97, 163, 163, 163, 163, 163, 163, 163, 1, 1, 1, 9, 42, 97, 97, 163, 163, 163, 1] 163
rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 429
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078120 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078120
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078120/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078120
Building REAL300000078121
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078121'
/scratch/stefan/7769659/working/building/REAL300000078121 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078121

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078121/0 /scratch/stefan/7769659/working/building/REAL300000078121 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/151
`/scratch/stefan/7769659/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCC(=O)[O-])

`REAL300000078121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078121 none CCOC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 73, 42, 42, 42, 19, 19, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 128, 197, 199, 199, 79, 79, 79, 79, 79, 42, 19, 12, 3, 3, 1, 1, 1, 42, 42, 197, 197] 201
rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42])
total number of confs: 691
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078121 none CCOC1=CC(C=NNCC2=CC=CC(Cl)=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 7, 7, 11, 36, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 7, 21, 35, 35, 5, 5, 5, 5, 5, 1, 7, 11, 36, 36, 42, 42, 42, 1, 1, 21, 21] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 18, 19, 20, 21, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078121 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078121
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078121/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078121
Building REAL300000078122
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078122'
/scratch/stefan/7769659/working/building/REAL300000078122 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078122

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078122/0 /scratch/stefan/7769659/working/building/REAL300000078122 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/152
`/scratch/stefan/7769659/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078122 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 19, 55, 110, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 55, 110, 110, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 505
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078122 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 15, 40, 79, 79, 79, 79, 79, 79, 79, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 15, 40, 40, 79, 79, 79] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 35] set([7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078122 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 201, 201, 201, 201, 201, 79, 74, 74, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 74, 31, 6, 6, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 510
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078122 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078122
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078122/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078122
Building REAL300000078123
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078123'
/scratch/stefan/7769659/working/building/REAL300000078123 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078123

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078123/0 /scratch/stefan/7769659/working/building/REAL300000078123 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/153
`/scratch/stefan/7769659/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-])

`REAL300000078123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078123 none COC1=CC=C(C)C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 90, 90, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 90, 35, 6, 6, 1, 1, 1] 137
rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 260
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078123 none COC1=CC=C(C)C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 79, 137, 137, 137, 137, 137, 137, 137, 1, 1, 2, 2, 4, 4, 4, 1, 1, 2, 2, 2, 5, 23, 79, 79, 137, 137, 137] 137
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078123 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078123
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078123/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078123
Building REAL300000078124
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078124'
/scratch/stefan/7769659/working/building/REAL300000078124 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078124

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078124/0 /scratch/stefan/7769659/working/building/REAL300000078124 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/154
`/scratch/stefan/7769659/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-])

`REAL300000078124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078124 none CN1C2=CC=C(F)C=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 37, 37, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 37, 25, 6, 6, 1, 1, 1] 47
rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078124 none CN1C2=CC=C(F)C=C2C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 29, 47, 47, 47, 47, 47, 47, 47, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 9, 29, 29, 47, 47, 47] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078124 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078124
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078124/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078124
Building REAL300000078125
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078125'
/scratch/stefan/7769659/working/building/REAL300000078125 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078125

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078125/0 /scratch/stefan/7769659/working/building/REAL300000078125 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/155
`/scratch/stefan/7769659/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1)

`REAL300000078125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078125 none O=C([O-])CCC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 174, 94, 94, 94, 94, 66, 66, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 174, 174, 94, 94, 66, 29, 6, 6, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 735
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078125 none O=C([O-])CCC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [21, 13, 13, 9, 1, 1, 1, 1, 1, 1, 4, 4, 13, 59, 94, 94, 94, 94, 94, 94, 94, 1, 13, 13, 9, 9, 1, 1, 4, 13, 59, 59, 94, 94, 94] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078125 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078125
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078125/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078125
Building REAL300000078126
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078126'
/scratch/stefan/7769659/working/building/REAL300000078126 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078126

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078126/0 /scratch/stefan/7769659/working/building/REAL300000078126 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/156
`/scratch/stefan/7769659/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=CC=C1)

`REAL300000078126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078126 none O=C([O-])C1=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 121, 121, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 121, 35, 8, 8, 1, 1, 1, 201, 201, 201] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 359
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078126 none O=C([O-])C1=C2NC=C(C=NNCC3=CC=CC(Cl)=C3Cl)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 46, 118, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 45, 118, 118, 201, 201, 201, 1, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 23, 24, 25, 33] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 529
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078126 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078126
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078126/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078126
Building REAL300000078127
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078127'
/scratch/stefan/7769659/working/building/REAL300000078127 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078127

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078127/0 /scratch/stefan/7769659/working/building/REAL300000078127 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/157
`/scratch/stefan/7769659/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=C2O1)

`REAL300000078127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078127 none O=C([O-])C1=CC2=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
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, 120, 120, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 120, 38, 8, 8, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 369
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078127 none O=C([O-])C1=CC2=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 51, 114, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 51, 114, 114, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078127 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078127
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078127/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078127
Building REAL300000078128
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078128'
/scratch/stefan/7769659/working/building/REAL300000078128 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078128

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078128/0 /scratch/stefan/7769659/working/building/REAL300000078128 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/158
`/scratch/stefan/7769659/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=CN12)

`REAL300000078128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078128 none O=C([O-])C1=CN=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [176, 176, 176, 176, 176, 176, 176, 128, 128, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 176, 128, 40, 8, 8, 1, 1, 1, 176, 176, 176] 176
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 306
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078128 none O=C([O-])C1=CN=C2C(C=NNCC3=CC=CC(Cl)=C3Cl)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 115, 176, 176, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 10, 49, 115, 115, 176, 176, 176, 1, 1, 1] 176
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 20, 21, 22, 23, 24, 33] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078128 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078128
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078128/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078128
Building REAL300000078129
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078129'
/scratch/stefan/7769659/working/building/REAL300000078129 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078129

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078129/0 /scratch/stefan/7769659/working/building/REAL300000078129 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/159
`/scratch/stefan/7769659/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078129 none O=C([O-])C1=C(F)C=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 37, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 37, 23, 6, 6, 1, 1, 1] 49
rigid atoms, others: [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, 12, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078129 none O=C([O-])C1=C(F)C=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 4, 4, 12, 29, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 12, 29, 29, 49, 49, 49] 49
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078129 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078129
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078129/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078129
Building REAL300000078130
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078130'
/scratch/stefan/7769659/working/building/REAL300000078130 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078130

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078130/0 /scratch/stefan/7769659/working/building/REAL300000078130 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/160
`/scratch/stefan/7769659/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078130 none O=C([O-])C1=CC=C2OCOC2=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 23, 21, 21, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 21, 17, 6, 6, 1, 1, 1] 23
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078130 none O=C([O-])C1=CC=C2OCOC2=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 4, 4, 10, 20, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 10, 20, 20, 23, 23, 23] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078130 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078130
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078130/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078130
Building REAL300000078131
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078131'
/scratch/stefan/7769659/working/building/REAL300000078131 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078131

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078131/0 /scratch/stefan/7769659/working/building/REAL300000078131 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/161
`/scratch/stefan/7769659/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1)

`REAL300000078131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078131 none N#CC1=CC=C(C(=O)[O-])C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 17, 6, 6, 1, 1, 1, 22] 22
rigid atoms, others: [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, 12, 32, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078131 none N#CC1=CC=C(C(=O)[O-])C(C=NNCC2=CC=CC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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, 2, 2, 1, 1, 4, 4, 11, 20, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 4, 11, 20, 20, 22, 22, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 22, 23, 24] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078131 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078131
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078131/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078131
Building REAL300000078132
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078132'
/scratch/stefan/7769659/working/building/REAL300000078132 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078132

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078132/0 /scratch/stefan/7769659/working/building/REAL300000078132 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/162
`/scratch/stefan/7769659/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1Cl)

`REAL300000078132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078132 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 166, 86, 62, 86, 86, 36, 36, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 201, 201, 86, 86, 36, 16, 5, 5, 1, 1, 1, 86] 201
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 565
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078132 none O=C([O-])COC1=CC=C(C=NNCC2=CC=CC(Cl)=C2Cl)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 25, 41, 7, 1, 1, 1, 1, 1, 1, 6, 6, 15, 70, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 25, 25, 1, 1, 6, 15, 70, 70, 86, 86, 86, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 407
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078132 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078132
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078132/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078132
Building REAL300000078133
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078133'
/scratch/stefan/7769659/working/building/REAL300000078133 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078133

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078133/0 /scratch/stefan/7769659/working/building/REAL300000078133 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/163
`/scratch/stefan/7769659/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-])

`REAL300000078133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078133 none CC1=NSC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1] 7
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 24
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078133 none CC1=NSC(C=NNCC2=CC=CC(Cl)=C2Cl)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 2, 2, 2, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7] 7
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078133 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078133
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078133/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078133
Building REAL300000078134
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078134'
/scratch/stefan/7769659/working/building/REAL300000078134 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078134

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078134/0 /scratch/stefan/7769659/working/building/REAL300000078134 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/164
`/scratch/stefan/7769659/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNCC3=CC=CC(Cl)=C3Cl)C(F)=CC=C2S1)

`REAL300000078134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078134 none O=C([O-])C1=CC2=C(C=NNCC3=CC=CC(Cl)=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 103, 103, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 103, 33, 6, 6, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 331
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078134 none O=C([O-])C1=CC2=C(C=NNCC3=CC=CC(Cl)=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 47, 121, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 11, 47, 121, 121, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 33] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31])
total number of confs: 538
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078134 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078134
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078134/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078134
Building REAL300000078135
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078135'
/scratch/stefan/7769659/working/building/REAL300000078135 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078135

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078135/0 /scratch/stefan/7769659/working/building/REAL300000078135 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/165
`/scratch/stefan/7769659/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl)

`REAL300000078135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078135 none COC1=CC(C(=O)[O-])=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 166, 167, 167, 167, 167, 167, 167, 167, 135, 135, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 135, 39, 8, 8, 1, 1, 1] 167
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])
total number of confs: 294
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078135 none COC1=CC(C(=O)[O-])=CC=C1C=NNCC1=CC=CC(Cl)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 115, 167, 167, 167, 167, 167, 167, 167, 4, 4, 4, 1, 1, 1, 6, 35, 115, 115, 167, 167, 167] 167
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 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: 492
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078135 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078135
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078135/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078135
Building REAL300000078136
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078136'
/scratch/stefan/7769659/working/building/REAL300000078136 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078136

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078136/0 /scratch/stefan/7769659/working/building/REAL300000078136 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/166
`/scratch/stefan/7769659/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=N2)C1)

`REAL300000078136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078136 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 21, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 12, 44, 82, 82, 82, 82, 82, 82, 82, 1, 11, 11, 11, 1, 1, 4, 12, 44, 44, 82, 82, 82, 11, 11] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 274
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078136 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 44, 124, 201, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 11, 11, 20, 44, 124, 124, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 25, 26, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 553
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078136 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNCC3=CC=CC(Cl)=C3Cl)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 82, 201, 82, 82, 82, 71, 71, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 82, 82, 71, 31, 6, 6, 1, 1, 1, 201, 201] 201
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 497
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078136 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078136
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078136/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078136
Building REAL300000078137
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078137'
/scratch/stefan/7769659/working/building/REAL300000078137 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078137

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078137/0 /scratch/stefan/7769659/working/building/REAL300000078137 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/167
`/scratch/stefan/7769659/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1)

`REAL300000078137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078137 none CCC(C)NN=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 93, 186, 49, 49, 4, 49, 4, 20, 20, 4, 1, 4, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 20, 20, 201, 201, 201, 201, 200, 186, 186, 183, 186, 92, 49, 49, 49, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 201
rigid atoms, others: [48, 49, 41, 42, 43, 12, 45, 46, 15, 16, 17, 18, 19, 22, 23, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51])
total number of confs: 799
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078137 none CCC(C)NN=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 74, 20, 74, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 32, 32, 20, 20, 1, 1, 98, 98, 98, 97, 97, 74, 74, 74, 74, 20, 6, 6, 6, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 201
rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 471
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078137 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078137
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078137/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078137
Building REAL300000078138
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078138'
/scratch/stefan/7769659/working/building/REAL300000078138 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078138

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078138/0 /scratch/stefan/7769659/working/building/REAL300000078138 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/168
`/scratch/stefan/7769659/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078138 none CCC(C)NN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 44, 9, 44, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 59, 59, 69, 69, 69, 69, 69, 44, 44, 44, 44, 9, 4, 1, 1, 1, 36, 36] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 482
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078138 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078138
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078138/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078138
Building REAL300000078139
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078139'
/scratch/stefan/7769659/working/building/REAL300000078139 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078139

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078139/0 /scratch/stefan/7769659/working/building/REAL300000078139 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/169
`/scratch/stefan/7769659/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1)

`REAL300000078139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078139 none CCC(C)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [163, 160, 75, 160, 47, 47, 20, 20, 19, 20, 20, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 20, 163, 163, 163, 163, 163, 160, 160, 160, 160, 75, 47, 19, 20, 20, 5, 5, 1, 1, 1, 1, 20] 163
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 607
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078139 none CCC(C)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [63, 54, 14, 54, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 8, 20, 20, 20, 20, 20, 20, 22, 22, 1, 63, 63, 63, 63, 63, 54, 54, 54, 54, 14, 6, 1, 1, 1, 8, 8, 20, 20, 20, 20, 1] 163
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 298
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078139 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078139
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078139/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078139
Building REAL300000078140
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078140'
/scratch/stefan/7769659/working/building/REAL300000078140 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078140

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078140/0 /scratch/stefan/7769659/working/building/REAL300000078140 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/170
`/scratch/stefan/7769659/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1)

`REAL300000078140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078140 none CCC(C)NN=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 179, 73, 179, 41, 41, 19, 19, 19, 19, 11, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 201, 201, 201, 201, 201, 179, 179, 179, 179, 73, 41, 19, 19, 9, 9, 1, 2, 2, 2, 19, 19] 201
rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 814
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078140 none CCC(C)NN=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 40, 10, 40, 5, 5, 1, 1, 1, 1, 1, 1, 2, 4, 19, 19, 19, 19, 19, 33, 33, 19, 1, 1, 54, 54, 54, 54, 54, 40, 40, 40, 40, 10, 5, 1, 1, 4, 4, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 44, 43, 22, 23] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 297
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078140 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078140
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078140/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078140
Building REAL300000078141
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078141'
/scratch/stefan/7769659/working/building/REAL300000078141 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078141

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078141/0 /scratch/stefan/7769659/working/building/REAL300000078141 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/171
`/scratch/stefan/7769659/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000078141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078141 none CCC(C)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 113, 201, 66, 66, 17, 17, 16, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 66, 16, 17, 17, 8, 8, 1, 1, 1, 1, 17] 201
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 721
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078141 none CCC(C)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 15, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 6, 1, 1, 1, 3, 3, 17, 17, 17, 17, 1] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078141 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078141
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078141/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078141
Building REAL300000078142
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078142'
/scratch/stefan/7769659/working/building/REAL300000078142 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078142

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078142/0 /scratch/stefan/7769659/working/building/REAL300000078142 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/172
`/scratch/stefan/7769659/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=C(Br)C=C(C(=O)[O-])N1C)

`REAL300000078142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078142 none CCC(C)NN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', '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, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 56, 30, 56, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 56, 56, 56, 56, 30, 12, 1, 2, 2, 2] 78
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078142 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078142
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078142/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078142
Building REAL300000078143
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078143'
/scratch/stefan/7769659/working/building/REAL300000078143 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078143

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078143/0 /scratch/stefan/7769659/working/building/REAL300000078143 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/173
`/scratch/stefan/7769659/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1)

`REAL300000078143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078143 none CCC(C)NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', '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, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 16, 64, 6, 6, 1, 1, 1, 1, 1, 1, 8, 30, 45, 45, 1, 1, 1, 81, 81, 81, 81, 81, 64, 64, 64, 64, 16, 6, 1, 1, 30, 30, 1] 201
rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 462
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078143 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078143
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078143/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078143
Building REAL300000078144
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078144'
/scratch/stefan/7769659/working/building/REAL300000078144 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078144

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078144/0 /scratch/stefan/7769659/working/building/REAL300000078144 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/174
`/scratch/stefan/7769659/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1)

`REAL300000078144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078144 none CCC(C)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 201, 126, 124, 56, 45, 88, 88, 45, 15, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 124, 88, 88, 15, 15, 8, 8, 1, 88] 201
rigid atoms, others: [42, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43])
total number of confs: 835
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078144 none CCC(C)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 11, 30, 6, 6, 1, 1, 1, 1, 1, 1, 9, 29, 34, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 32, 32, 32, 32, 32, 30, 30, 30, 30, 11, 6, 1, 1, 29, 29, 34, 34, 88, 1] 201
rigid atoms, others: [43, 36, 37, 6, 7, 8, 9, 10, 11, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078144 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078144
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078144/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078144
Building REAL300000078145
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078145'
/scratch/stefan/7769659/working/building/REAL300000078145 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078145

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078145/0 /scratch/stefan/7769659/working/building/REAL300000078145 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/175
`/scratch/stefan/7769659/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(OC)=C(OCC(=O)[O-])C=C1[N+](=O)[O-])

`REAL300000078145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078145 none CCC(C)NN=CC1=CC(OC)=C(OCC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 14, 57, 5, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 17, 23, 23, 1, 1, 1, 2, 2, 73, 73, 73, 73, 73, 57, 57, 57, 57, 14, 5, 1, 3, 3, 3, 17, 17, 1] 201
rigid atoms, others: [34, 6, 7, 8, 9, 10, 12, 13, 40, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 11, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 365
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078145 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078145
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078145/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078145
Building REAL300000078146
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078146'
/scratch/stefan/7769659/working/building/REAL300000078146 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078146

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078146/0 /scratch/stefan/7769659/working/building/REAL300000078146 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/176
`/scratch/stefan/7769659/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-])

`REAL300000078146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078146 none CCC(C)NN=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [87, 62, 24, 62, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 16, 26, 26, 87, 87, 87, 87, 87, 62, 62, 62, 62, 24, 4, 1, 1, 1, 4, 4, 4, 16, 16] 131
rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41])
total number of confs: 428
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078146 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078146
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078146/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078146
Building REAL300000078147
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078147'
/scratch/stefan/7769659/working/building/REAL300000078147 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078147

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078147/0 /scratch/stefan/7769659/working/building/REAL300000078147 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/177
`/scratch/stefan/7769659/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)N=NC(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1)

`REAL300000078147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078147 none CCC(C)N=NC(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 27, 64, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 38, 38, 1, 1, 68, 68, 68, 68, 68, 64, 64, 64, 64, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 1, 1] 201
rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 20, 21, 46, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 357
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078147 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078147
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078147/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078147
Building REAL300000078148
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078148'
/scratch/stefan/7769659/working/building/REAL300000078148 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078148

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078148/0 /scratch/stefan/7769659/working/building/REAL300000078148 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/178
`/scratch/stefan/7769659/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)N=NC(C)CCC1=CC=C(OCCC(=O)[O-])C=C1)

`REAL300000078148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078148 none CCC(C)N=NC(C)CCC1=CC=C(OCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 49, 20, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 20, 28, 44, 37, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 20, 20, 28, 28, 1, 1] 201
rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 20, 21, 46, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 309
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078148 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078148
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078148/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078148
Building REAL300000078149
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078149'
/scratch/stefan/7769659/working/building/REAL300000078149 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078149

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078149/0 /scratch/stefan/7769659/working/building/REAL300000078149 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/179
`/scratch/stefan/7769659/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)N=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000078149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078149 none CCC(C)N=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 174, 59, 20, 59, 16, 8, 8, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 201, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 59, 20, 20, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [48, 51, 49, 50, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53])
total number of confs: 603
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078149 none CCC(C)N=NC(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 24, 32, 24, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 16, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [45, 11, 8, 9, 10, 43, 12, 13, 14, 44, 52, 53, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078149 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078149
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078149/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078149
Building REAL300000078150
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078150'
/scratch/stefan/7769659/working/building/REAL300000078150 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078150

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078150/0 /scratch/stefan/7769659/working/building/REAL300000078150 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/180
`/scratch/stefan/7769659/working/3D/180' -> `0.mol2'
Preparing input files

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

`REAL300000078150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078150 none CCC(=NNC(C)CC)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 7, 7, 17, 40, 40, 41, 1, 1, 1, 1, 1, 6, 10, 23, 26, 43, 49, 51, 1, 1, 10, 10, 10, 10, 10, 17, 40, 40, 40, 40, 41, 41, 41, 41, 41, 1, 1, 10, 10, 22, 22, 27, 27, 42, 42, 1, 1] 201
rigid atoms, others: [2, 38, 39, 9, 10, 11, 12, 13, 48, 49, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 394
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078150 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078150
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078150/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078150
Building REAL300000078151
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078151'
/scratch/stefan/7769659/working/building/REAL300000078151 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078151

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078151/0 /scratch/stefan/7769659/working/building/REAL300000078151 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/181
`/scratch/stefan/7769659/working/3D/181' -> `0.mol2'
Preparing input files

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

`REAL300000078151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078151 none CCC(C)NN=C(C)C1=CC=C(OCCCC(=O)[O-])C(OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 51, 9, 9, 1, 9, 1, 1, 1, 1, 1, 10, 24, 27, 36, 48, 48, 1, 1, 3, 1, 52, 52, 52, 52, 51, 51, 51, 51, 51, 20, 9, 9, 9, 1, 1, 24, 24, 27, 27, 36, 36, 3, 3, 3, 1] 201
rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 47, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 391
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078151 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078151
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078151/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078151
Building REAL300000078152
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078152'
/scratch/stefan/7769659/working/building/REAL300000078152 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078152

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078152/0 /scratch/stefan/7769659/working/building/REAL300000078152 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/182
`/scratch/stefan/7769659/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078152 none CCC(C)NN=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 57, 19, 57, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 54, 54, 79, 79, 79, 79, 79, 57, 57, 57, 57, 19, 7, 7, 7, 1, 1, 1, 33, 33] 201
rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 481
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078152 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078152
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078152/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078152
Building REAL300000078153
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078153'
/scratch/stefan/7769659/working/building/REAL300000078153 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078153

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078153/0 /scratch/stefan/7769659/working/building/REAL300000078153 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/183
`/scratch/stefan/7769659/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000078153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078153 none CCC(C)NN=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [139, 115, 46, 115, 9, 9, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 115, 115, 115, 115, 46, 10, 10, 10, 2, 2, 1, 1, 2, 2, 2, 1] 142
rigid atoms, others: [37, 6, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41])
total number of confs: 572
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078153 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078153
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078153/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078153
Building REAL300000078154
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078154'
/scratch/stefan/7769659/working/building/REAL300000078154 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078154

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078154/0 /scratch/stefan/7769659/working/building/REAL300000078154 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/184
`/scratch/stefan/7769659/working/3D/184' -> `0.mol2'
Preparing input files

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

`REAL300000078154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078154 none CCC(C)NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 113, 201, 77, 77, 45, 45, 45, 45, 45, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 77, 45, 45, 45, 3, 1, 1, 1, 1, 1, 45] 201
rigid atoms, others: [39, 40, 41, 42, 43, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44])
total number of confs: 723
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078154 none CCC(C)NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 8, 28, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 32, 42, 42, 32, 45, 45, 32, 45, 45, 1, 30, 30, 30, 30, 30, 28, 28, 28, 28, 8, 4, 1, 1, 1, 32, 45, 45, 32, 45, 45, 1] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 322
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078154 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078154
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078154/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078154
Building REAL300000078155
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078155'
/scratch/stefan/7769659/working/building/REAL300000078155 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078155

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078155/0 /scratch/stefan/7769659/working/building/REAL300000078155 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/185
`/scratch/stefan/7769659/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C1)

`REAL300000078155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078155 none CCC(C)NN=CC1=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', '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, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 15, 64, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 19, 19, 1, 1, 3, 1, 77, 77, 77, 77, 77, 64, 64, 64, 64, 15, 6, 1, 13, 14, 14, 14, 4, 4, 4, 1] 201
rigid atoms, others: [33, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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
/scratch/stefan/7769659/working/building/REAL300000078155 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078155
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078155/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078155
Building REAL300000078156
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078156'
/scratch/stefan/7769659/working/building/REAL300000078156 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078156

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078156/0 /scratch/stefan/7769659/working/building/REAL300000078156 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/186
`/scratch/stefan/7769659/working/3D/186' -> `0.mol2'
Preparing input files

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

`REAL300000078156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078156 none CCC(C)NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 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', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 193, 110, 193, 49, 49, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 193, 193, 193, 193, 110, 49, 12, 12, 1, 1, 2, 1] 402
rigid atoms, others: [35, 36, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37])
total number of confs: 720
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078156 none CCC(C)NN=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 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', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [123, 86, 28, 86, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 123, 123, 123, 123, 123, 86, 86, 86, 86, 28, 7, 1, 1, 12, 12, 24, 12] 402
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 21] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078156 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078156
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078156/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078156
Building REAL300000078157
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078157'
/scratch/stefan/7769659/working/building/REAL300000078157 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078157

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078157/0 /scratch/stefan/7769659/working/building/REAL300000078157 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/187
`/scratch/stefan/7769659/working/3D/187' -> `0.mol2'
Preparing input files

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

`REAL300000078157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078157 none CCC(C)NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 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', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 106, 193, 54, 54, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 193, 193, 193, 193, 106, 54, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078157 none CCC(C)NN=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 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', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 79, 28, 79, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 110, 110, 110, 110, 110, 79, 79, 79, 79, 27, 6, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 20] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 447
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078157 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078157
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078157/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078157
Building REAL300000078158
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078158'
/scratch/stefan/7769659/working/building/REAL300000078158 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078158

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078158/0 /scratch/stefan/7769659/working/building/REAL300000078158 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/188
`/scratch/stefan/7769659/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O)

`REAL300000078158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078158 none CCC(C)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [76, 50, 28, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 50, 50, 50, 50, 28, 11, 1, 1, 2] 152
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 316
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078158 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078158/1 /scratch/stefan/7769659/working/building/REAL300000078158 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/189
`/scratch/stefan/7769659/working/3D/189' -> `1.mol2'
Preparing input files

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

`REAL300000078158.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078158/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078158 none CCC(C)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', '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, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [43, 29, 15, 29, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 29, 29, 29, 29, 15, 4, 1, 1] 43
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078158 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078158
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078158/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078158/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078158
Building REAL300000078159
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078159'
/scratch/stefan/7769659/working/building/REAL300000078159 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078159

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078159/0 /scratch/stefan/7769659/working/building/REAL300000078159 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/190
`/scratch/stefan/7769659/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-])

`REAL300000078159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078159 none CCC(C)NN=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 17, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 16, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 3, 13, 26, 26, 77, 77, 77, 77, 77, 50, 50, 50, 50, 16, 4, 1, 1, 4, 4, 4, 13, 13] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16] set([0, 1, 2, 3, 4, 5, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 398
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078159 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078159
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078159/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078159
Building REAL300000078160
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078160'
/scratch/stefan/7769659/working/building/REAL300000078160 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078160

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078160/0 /scratch/stefan/7769659/working/building/REAL300000078160 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/191
`/scratch/stefan/7769659/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078160 none CCC(C)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 103, 198, 61, 61, 33, 33, 33, 33, 20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 198, 198, 198, 198, 103, 61, 33, 33, 9, 9, 1, 1, 33, 33] 201
rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 723
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078160 none CCC(C)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 57, 19, 57, 5, 5, 1, 1, 1, 1, 1, 1, 2, 10, 33, 33, 33, 33, 33, 33, 33, 1, 1, 82, 82, 82, 82, 82, 57, 57, 57, 57, 19, 5, 1, 1, 10, 10, 33, 33, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 389
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078160 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078160
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078160/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078160
Building REAL300000078161
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078161'
/scratch/stefan/7769659/working/building/REAL300000078161 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078161

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078161/0 /scratch/stefan/7769659/working/building/REAL300000078161 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/192
`/scratch/stefan/7769659/working/3D/192' -> `0.mol2'
Preparing input files

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

`REAL300000078161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078161 none CCC(C)NN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 18, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 45, 23, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 45, 45, 45, 45, 23, 8, 1, 1, 1] 65
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078161 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078161
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078161/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078161
Building REAL300000078162
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078162'
/scratch/stefan/7769659/working/building/REAL300000078162 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078162

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078162/0 /scratch/stefan/7769659/working/building/REAL300000078162 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/193
`/scratch/stefan/7769659/working/3D/193' -> `0.mol2'
Preparing input files

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

`REAL300000078162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078162 none CCC(C)NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [126, 114, 52, 114, 16, 12, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 126, 126, 126, 126, 126, 114, 114, 114, 114, 52, 12, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201
rigid atoms, others: [36, 37, 41, 10, 11, 12, 13, 14, 15, 16, 20, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43])
total number of confs: 496
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078162 none CCC(C)NN=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 17, 40, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 22, 22, 5, 1, 1, 51, 51, 51, 51, 51, 40, 40, 40, 40, 16, 5, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 43, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078162 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078162
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078162/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078162
Building REAL300000078163
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078163'
/scratch/stefan/7769659/working/building/REAL300000078163 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078163

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078163/0 /scratch/stefan/7769659/working/building/REAL300000078163 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/194
`/scratch/stefan/7769659/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=C(C(=O)[O-])C=C(Br)S1)

`REAL300000078163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078163 none CCC(C)NN=CC1=C(C(=O)[O-])C=C(Br)S1 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', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', '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, 11, 11, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [57, 37, 20, 37, 3, 3, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 57, 57, 57, 57, 57, 37, 37, 37, 37, 19, 3, 1] 70
rigid atoms, others: [6, 7, 8, 9, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078163 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078163
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078163/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078163
Building REAL300000078164
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078164'
/scratch/stefan/7769659/working/building/REAL300000078164 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078164

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078164/0 /scratch/stefan/7769659/working/building/REAL300000078164 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/195
`/scratch/stefan/7769659/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)

`REAL300000078164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078164 none CCC(C)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', '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, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 118, 201, 106, 106, 99, 99, 99, 99, 99, 99, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 106, 99, 99, 99, 99, 9, 9, 1, 1] 201
rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 635
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078164 none CCC(C)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', '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, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 8, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 99, 99, 99, 99, 99, 99, 99, 23, 23, 23, 23, 23, 21, 21, 21, 21, 8, 4, 1, 1, 1, 1, 32, 32, 99, 99] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 278
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078164 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078164
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078164/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078164
Building REAL300000078165
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078165'
/scratch/stefan/7769659/working/building/REAL300000078165 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078165

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078165/0 /scratch/stefan/7769659/working/building/REAL300000078165 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/196
`/scratch/stefan/7769659/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000078165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078165 none CCC(C)NN=CC1=CC=C(S(=O)(=O)NCC(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [28, 21, 7, 21, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 28, 28, 28, 28, 28, 21, 21, 21, 21, 7, 3, 1, 1, 9, 17, 17, 1, 1] 99
rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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
/scratch/stefan/7769659/working/building/REAL300000078165 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078165
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078165/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078165
Building REAL300000078166
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078166'
/scratch/stefan/7769659/working/building/REAL300000078166 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078166

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078166/0 /scratch/stefan/7769659/working/building/REAL300000078166 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/197
`/scratch/stefan/7769659/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=C1)

`REAL300000078166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078166 none COC1=CC=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 51, 51, 51, 51, 51, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 57, 57, 51, 75, 75, 75, 51, 51, 51, 16, 5, 1, 1, 1, 1, 31, 31, 51] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 314
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078166 none COC1=CC=CC(NN=CC2=CC=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 51, 51, 25, 51, 51, 51, 111, 164, 170, 170, 1, 3, 3, 3, 1, 1, 1, 7, 25, 51, 51, 51, 51, 164, 164, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 569
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078166 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078166
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078166/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078166
Building REAL300000078167
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078167'
/scratch/stefan/7769659/working/building/REAL300000078167 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078167

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078167/0 /scratch/stefan/7769659/working/building/REAL300000078167 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/198
`/scratch/stefan/7769659/working/3D/198' -> `0.mol2'
Preparing input files

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

`REAL300000078167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078167 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 45, 45, 45, 45, 16, 4, 4, 1, 1, 1, 1, 1, 1, 5, 21, 37, 37, 1, 1, 45, 67, 67, 67, 45, 45, 45, 16, 4, 1, 1, 21, 21, 1, 1, 45] 201
rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36])
total number of confs: 238
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078167 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 26, 26, 45, 45, 27, 35, 109, 165, 177, 177, 45, 45, 1, 3, 3, 3, 1, 1, 1, 6, 26, 45, 45, 165, 165, 45, 45, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 592
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078167 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078167
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078167/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078167
Building REAL300000078168
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078168'
/scratch/stefan/7769659/working/building/REAL300000078168 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078168

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078168/0 /scratch/stefan/7769659/working/building/REAL300000078168 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/199
`/scratch/stefan/7769659/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1)

`REAL300000078168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078168 none COC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 51, 51, 51, 51, 51, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 33, 55, 55, 51, 78, 78, 78, 51, 51, 51, 14, 4, 1, 1, 1, 33, 33, 51] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 314
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078168 none COC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 51, 51, 51, 28, 51, 51, 51, 110, 171, 180, 180, 1, 3, 3, 3, 1, 1, 1, 9, 28, 51, 51, 51, 171, 171, 1] 201
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: 606
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078168 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078168
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078168/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078168
Building REAL300000078169
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078169'
/scratch/stefan/7769659/working/building/REAL300000078169 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078169

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078169/0 /scratch/stefan/7769659/working/building/REAL300000078169 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/200
`/scratch/stefan/7769659/working/3D/200' -> `0.mol2'
Preparing input files

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

`REAL300000078169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078169 none COC1=CC=CC(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 45, 45, 44, 45, 45, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 37, 37, 1, 45, 65, 65, 65, 44, 45, 45, 16, 6, 1, 1, 1, 26, 26, 26, 26, 1, 45] 201
rigid atoms, others: [32, 33, 38, 9, 10, 11, 12, 13, 14, 15, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 39])
total number of confs: 242
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078169 none COC1=CC=CC(NN=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 45, 45, 45, 45, 45, 122, 170, 170, 183, 183, 45, 1, 3, 3, 3, 1, 1, 1, 7, 23, 45, 45, 45, 170, 170, 170, 170, 45, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 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, 36, 37, 38])
total number of confs: 495
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078169 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078169
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078169/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078169
Building REAL300000078170
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078170'
/scratch/stefan/7769659/working/building/REAL300000078170 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078170

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078170/0 /scratch/stefan/7769659/working/building/REAL300000078170 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/201
`/scratch/stefan/7769659/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1)

`REAL300000078170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078170 none COC1=CC=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 43, 43, 42, 43, 43, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 19, 27, 40, 34, 1, 43, 59, 59, 59, 42, 43, 43, 14, 6, 1, 1, 1, 19, 19, 27, 27, 1, 43] 201
rigid atoms, others: [32, 33, 38, 9, 10, 11, 12, 13, 14, 15, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 39])
total number of confs: 249
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078170 none COC1=CC=CC(NN=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 43, 43, 43, 43, 43, 116, 150, 163, 182, 180, 43, 1, 3, 3, 3, 1, 1, 1, 7, 18, 43, 43, 43, 150, 150, 163, 163, 43, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 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, 36, 37, 38])
total number of confs: 500
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078170 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078170
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078170/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078170
Building REAL300000078171
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078171'
/scratch/stefan/7769659/working/building/REAL300000078171 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078171

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078171/0 /scratch/stefan/7769659/working/building/REAL300000078171 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/202
`/scratch/stefan/7769659/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1)

`REAL300000078171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078171 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [81, 51, 51, 50, 51, 51, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 6, 16, 16, 15, 16, 16, 16, 18, 18, 1, 51, 81, 81, 81, 50, 51, 51, 14, 6, 1, 1, 1, 6, 6, 16, 16, 15, 16, 1, 51] 201
rigid atoms, others: [45, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 46])
total number of confs: 196
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078171 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 51, 51, 51, 51, 51, 75, 85, 163, 163, 163, 163, 163, 163, 201, 201, 51, 1, 2, 2, 2, 1, 1, 1, 7, 19, 51, 51, 51, 85, 85, 163, 163, 163, 163, 51, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 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, 42, 43, 44, 45])
total number of confs: 448
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078171 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 163, 163, 163, 163, 159, 78, 47, 47, 16, 16, 16, 16, 16, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 163, 201, 201, 201, 163, 163, 163, 78, 47, 16, 15, 16, 6, 6, 1, 1, 1, 1, 16, 163] 201
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 448
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078171 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078171
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078171/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078171
Building REAL300000078172
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078172'
/scratch/stefan/7769659/working/building/REAL300000078172 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078172

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078172/0 /scratch/stefan/7769659/working/building/REAL300000078172 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/203
`/scratch/stefan/7769659/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1)

`REAL300000078172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078172 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [46, 37, 37, 37, 37, 37, 15, 7, 7, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 37, 46, 46, 46, 37, 37, 37, 15, 7, 1, 1, 5, 5, 1, 37] 57
rigid atoms, others: [33, 34, 37, 9, 10, 11, 12, 13, 14, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078172 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 7, 13, 13, 37, 37, 13, 13, 47, 57, 57, 57, 37, 37, 37, 37, 37, 1, 3, 3, 3, 1, 1, 1, 7, 13, 37, 37, 57, 57, 37, 1] 57
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 38, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 209
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078172 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078172
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078172/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078172
Building REAL300000078173
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078173'
/scratch/stefan/7769659/working/building/REAL300000078173 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078173

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078173/0 /scratch/stefan/7769659/working/building/REAL300000078173 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/204
`/scratch/stefan/7769659/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1)

`REAL300000078173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078173 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 34, 34, 34, 34, 14, 4, 4, 1, 1, 1, 1, 1, 1, 2, 4, 19, 19, 19, 19, 19, 35, 35, 19, 1, 1, 34, 48, 48, 48, 34, 34, 34, 14, 4, 1, 1, 4, 4, 19, 19, 19, 19, 1, 1, 34] 201
rigid atoms, others: [45, 36, 37, 9, 10, 11, 12, 13, 14, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46])
total number of confs: 182
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078173 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 34, 34, 20, 28, 50, 52, 150, 150, 150, 150, 150, 201, 201, 150, 34, 34, 1, 3, 3, 3, 1, 1, 1, 6, 19, 34, 34, 52, 52, 150, 150, 150, 150, 34, 34, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 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, 42, 43, 44, 45])
total number of confs: 502
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078173 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 150, 150, 150, 150, 150, 71, 39, 39, 19, 19, 19, 19, 11, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 150, 201, 201, 201, 150, 150, 150, 71, 39, 18, 19, 9, 9, 1, 2, 2, 2, 19, 19, 150] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 429
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078173 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078173
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078173/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078173
Building REAL300000078174
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078174'
/scratch/stefan/7769659/working/building/REAL300000078174 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078174

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078174/0 /scratch/stefan/7769659/working/building/REAL300000078174 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/205
`/scratch/stefan/7769659/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1)

`REAL300000078174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078174 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [41, 34, 34, 33, 34, 34, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 16, 16, 16, 15, 1, 34, 41, 41, 41, 33, 34, 34, 14, 6, 1, 1, 1, 2, 2, 16, 16, 15, 16, 1, 34] 201
rigid atoms, others: [45, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 46])
total number of confs: 114
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078174 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 34, 34, 34, 34, 34, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 34, 1, 2, 2, 2, 1, 1, 1, 7, 15, 34, 34, 34, 58, 58, 201, 201, 201, 201, 34, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 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, 42, 43, 44, 45])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078174 none COC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 102, 57, 57, 16, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 201, 201, 201, 201, 201, 201, 201, 102, 57, 15, 15, 15, 8, 8, 1, 1, 1, 1, 16, 201] 201
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 459
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078174 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078174
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078174/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078174
Building REAL300000078175
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078175'
/scratch/stefan/7769659/working/building/REAL300000078175 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078175

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078175/0 /scratch/stefan/7769659/working/building/REAL300000078175 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/206
`/scratch/stefan/7769659/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=C1)

`REAL300000078175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078175 none COC1=CC=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 44, 44, 43, 44, 44, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 20, 29, 29, 1, 44, 61, 61, 61, 43, 44, 44, 14, 6, 1, 1, 1, 20, 20, 1, 44] 201
rigid atoms, others: [32, 35, 9, 10, 11, 12, 13, 14, 15, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36])
total number of confs: 200
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078175 none COC1=CC=CC(NN=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 44, 44, 44, 44, 44, 105, 163, 179, 179, 44, 1, 2, 2, 2, 1, 1, 1, 7, 21, 44, 44, 44, 163, 163, 44, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 521
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078175 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078175
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078175/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078175
Building REAL300000078176
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078176'
/scratch/stefan/7769659/working/building/REAL300000078176 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078176

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078176/0 /scratch/stefan/7769659/working/building/REAL300000078176 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/207
`/scratch/stefan/7769659/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=C1)

`REAL300000078176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078176 none COC1=CC=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 31, 31, 31, 31, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 8, 38, 65, 65, 31, 48, 48, 48, 31, 31, 31, 8, 4, 1, 1, 2, 2, 2, 1, 38, 38, 31] 201
rigid atoms, others: [32, 33, 37, 9, 10, 11, 12, 13, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40])
total number of confs: 297
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078176 none COC1=CC=CC(NN=CC2=CC=C(OC)C=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 31, 31, 18, 31, 47, 31, 31, 31, 87, 177, 190, 190, 1, 2, 2, 2, 1, 1, 1, 7, 18, 31, 31, 47, 47, 47, 31, 177, 177, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 670
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078176 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078176
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078176/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078176
Building REAL300000078177
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078177'
/scratch/stefan/7769659/working/building/REAL300000078177 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078177

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078177/0 /scratch/stefan/7769659/working/building/REAL300000078177 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/208
`/scratch/stefan/7769659/working/3D/208' -> `0.mol2'
Preparing input files

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

`REAL300000078177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078177 none COC1=CC=CC(NN=CC2=CC=C(OC(F)(F)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.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 21, 21, 21, 21, 8, 4, 4, 1, 1, 1, 1, 1, 1, 12, 44, 44, 43, 64, 64, 1, 1, 21, 31, 31, 31, 21, 21, 21, 8, 4, 1, 1, 1, 1, 21] 201
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078177 none COC1=CC=CC(NN=CC2=CC=C(OC(F)(F)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.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 21, 21, 13, 19, 109, 169, 171, 171, 188, 188, 21, 21, 1, 3, 3, 3, 1, 1, 1, 6, 12, 21, 21, 21, 21, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 36, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35])
total number of confs: 545
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078177 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078177
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078177/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078177
Building REAL300000078178
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078178'
/scratch/stefan/7769659/working/building/REAL300000078178 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078178

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078178/0 /scratch/stefan/7769659/working/building/REAL300000078178 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/209
`/scratch/stefan/7769659/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1)

`REAL300000078178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078178 none COC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 64, 64, 64, 64, 64, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 80, 80, 80, 64, 64, 64, 39, 12, 1, 2, 2, 2, 64] 80
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078178 none COC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 1, 11, 44, 44, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 2, 2, 2, 1, 1, 1, 11, 44, 64, 64, 64, 64, 1] 80
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078178 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078178
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078178/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078178
Building REAL300000078179
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078179'
/scratch/stefan/7769659/working/building/REAL300000078179 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078179

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078179/0 /scratch/stefan/7769659/working/building/REAL300000078179 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/210
`/scratch/stefan/7769659/working/3D/210' -> `0.mol2'
Preparing input files

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

`REAL300000078179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078179 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 58, 58, 58, 58, 58, 19, 7, 7, 1, 1, 1, 1, 1, 1, 7, 30, 48, 48, 1, 1, 1, 58, 85, 85, 85, 58, 58, 58, 19, 7, 1, 1, 30, 30, 1, 58] 201
rigid atoms, others: [32, 35, 9, 10, 11, 12, 13, 14, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 318
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078179 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 57, 58, 35, 35, 125, 190, 192, 192, 58, 58, 58, 1, 3, 3, 3, 1, 1, 1, 7, 23, 58, 58, 190, 190, 58, 1] 201
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: 585
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078179 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078179
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078179/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078179
Building REAL300000078180
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078180'
/scratch/stefan/7769659/working/building/REAL300000078180 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078180

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078180/0 /scratch/stefan/7769659/working/building/REAL300000078180 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/211
`/scratch/stefan/7769659/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1)

`REAL300000078180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078180 none COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 104, 104, 104, 104, 104, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 104, 139, 139, 139, 104, 104, 104, 32, 7, 1, 4, 4, 4, 1, 1, 104] 139
rigid atoms, others: [33, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 39])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078180 none COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 1, 1, 1, 1, 1, 1, 13, 59, 59, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 139, 104, 104, 1, 3, 3, 3, 1, 1, 1, 13, 59, 104, 139, 139, 139, 104, 104, 1] 139
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078180 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078180
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078180/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078180
Building REAL300000078181
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078181'
/scratch/stefan/7769659/working/building/REAL300000078181 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078181

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078181/0 /scratch/stefan/7769659/working/building/REAL300000078181 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/212
`/scratch/stefan/7769659/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=C1)

`REAL300000078181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078181 none COC1=CC=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 65, 65, 65, 65, 65, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 74, 74, 74, 65, 65, 65, 29, 8, 1, 1, 1, 1, 65] 74
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078181 none COC1=CC=CC(NN=CC2=C3C=CC(C(=O)[O-])=CC3=NN2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 46, 46, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 3, 3, 3, 1, 1, 1, 11, 46, 65, 65, 65, 65, 1] 74
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 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])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078181 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078181/1 /scratch/stefan/7769659/working/building/REAL300000078181 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/213
`/scratch/stefan/7769659/working/3D/213' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=C1)

`REAL300000078181.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078181/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078181 none COC1=CC=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 96, 96, 95, 96, 96, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 106, 106, 106, 95, 96, 96, 43, 12, 1, 1, 1, 1, 96] 106
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078181 none COC1=CC=CC(NN=CC2=NNC3=CC(C(=O)[O-])=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 50, 50, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 3, 3, 3, 1, 1, 1, 11, 50, 96, 96, 96, 96, 1] 106
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 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])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078181 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078181
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078181/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078181/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078181
Building REAL300000078182
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078182'
/scratch/stefan/7769659/working/building/REAL300000078182 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078182

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078182/0 /scratch/stefan/7769659/working/building/REAL300000078182 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/214
`/scratch/stefan/7769659/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1)

`REAL300000078182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078182 none COC1=CC=CC(NN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 50, 50, 50, 50, 16, 6, 6, 1, 1, 1, 1, 1, 3, 1, 1, 8, 15, 21, 21, 1, 1, 1, 2, 2, 50, 73, 73, 73, 50, 50, 50, 16, 6, 1, 3, 3, 3, 15, 15, 1, 50] 201
rigid atoms, others: [35, 9, 10, 11, 12, 13, 15, 16, 21, 22, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42])
total number of confs: 209
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078182 none COC1=CC=CC(NN=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 50, 50, 50, 91, 50, 50, 148, 179, 183, 183, 50, 50, 50, 50, 50, 1, 3, 3, 3, 1, 1, 1, 7, 21, 50, 91, 91, 91, 179, 179, 50, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 42, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 493
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078182 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078182
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078182/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078182
Building REAL300000078183
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078183'
/scratch/stefan/7769659/working/building/REAL300000078183 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078183

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078183/0 /scratch/stefan/7769659/working/building/REAL300000078183 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/215
`/scratch/stefan/7769659/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1)

`REAL300000078183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078183 none COC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [79, 59, 59, 59, 59, 59, 14, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 15, 25, 25, 59, 79, 79, 79, 59, 59, 59, 14, 4, 1, 1, 1, 4, 4, 4, 15, 15, 59] 119
rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 218
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078183 none COC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 11, 42, 42, 59, 59, 59, 59, 59, 59, 43, 59, 59, 59, 73, 73, 118, 119, 119, 1, 3, 3, 3, 1, 1, 1, 11, 42, 59, 59, 59, 73, 73, 73, 118, 118, 1] 119
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 443
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078183 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078183
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078183/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078183
Building REAL300000078184
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078184'
/scratch/stefan/7769659/working/building/REAL300000078184 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078184

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078184/0 /scratch/stefan/7769659/working/building/REAL300000078184 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/216
`/scratch/stefan/7769659/working/3D/216' -> `0.mol2'
Preparing input files

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

`REAL300000078184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078184 none COC1=CC=CC(NN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 37, 37, 37, 37, 15, 7, 7, 1, 1, 1, 1, 1, 1, 9, 20, 20, 36, 34, 1, 1, 3, 1, 37, 51, 51, 51, 37, 37, 37, 15, 7, 1, 1, 20, 20, 20, 20, 4, 4, 4, 1, 37] 201
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 20, 21, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078184 none COC1=CC=CC(NN=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 37, 37, 37, 37, 109, 160, 160, 188, 179, 37, 37, 64, 36, 1, 3, 3, 3, 1, 1, 1, 7, 13, 37, 37, 160, 160, 160, 160, 64, 64, 64, 37, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 43, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 583
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078184 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078184
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078184/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078184
Building REAL300000078185
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078185'
/scratch/stefan/7769659/working/building/REAL300000078185 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078185

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078185/0 /scratch/stefan/7769659/working/building/REAL300000078185 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/217
`/scratch/stefan/7769659/working/3D/217' -> `0.mol2'
Preparing input files

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

`REAL300000078185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078185 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 47, 47, 47, 47, 47, 30, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 59, 59, 59, 47, 47, 47, 30, 10, 1, 1, 1, 47] 59
rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 20, 21, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078185 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 47, 47, 45, 47, 47, 47, 47, 47, 47, 1, 3, 3, 3, 1, 1, 1, 11, 37, 47, 47, 47, 1] 59
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 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
/scratch/stefan/7769659/working/building/REAL300000078185 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078185
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078185/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078185
Building REAL300000078186
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078186'
/scratch/stefan/7769659/working/building/REAL300000078186 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078186

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078186/0 /scratch/stefan/7769659/working/building/REAL300000078186 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/218
`/scratch/stefan/7769659/working/3D/218' -> `0.mol2'
Preparing input files

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

`REAL300000078186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078186 none COC1=CC=CC(NN=CC2=CC=C(OC(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.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 44, 44, 44, 44, 14, 4, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 37, 37, 1, 1, 44, 65, 65, 65, 44, 44, 44, 14, 4, 1, 1, 27, 27, 27, 27, 1, 1, 44] 201
rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 231
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078186 none COC1=CC=CC(NN=CC2=CC=C(OC(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.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 23, 24, 44, 44, 24, 34, 121, 173, 173, 185, 185, 44, 44, 1, 3, 3, 3, 1, 1, 1, 6, 23, 44, 44, 170, 173, 173, 172, 44, 44, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 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, 36, 37, 38])
total number of confs: 589
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078186 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078186
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078186/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078186
Building REAL300000078187
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078187'
/scratch/stefan/7769659/working/building/REAL300000078187 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078187

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078187/0 /scratch/stefan/7769659/working/building/REAL300000078187 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/219
`/scratch/stefan/7769659/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1)

`REAL300000078187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078187 none COC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [126, 92, 92, 92, 92, 92, 32, 6, 6, 1, 1, 1, 1, 1, 8, 17, 17, 1, 1, 1, 1, 1, 1, 92, 126, 126, 126, 92, 92, 92, 32, 6, 1, 8, 8, 1, 1, 1, 1, 92] 201
rigid atoms, others: [32, 35, 36, 37, 38, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 39])
total number of confs: 279
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078187 none COC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 10, 38, 38, 92, 92, 92, 177, 189, 189, 92, 92, 92, 92, 92, 92, 1, 2, 2, 2, 1, 1, 1, 10, 38, 92, 177, 177, 92, 92, 92, 92, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078187 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078187
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078187/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078187
Building REAL300000078188
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078188'
/scratch/stefan/7769659/working/building/REAL300000078188 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078188

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078188/0 /scratch/stefan/7769659/working/building/REAL300000078188 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/220
`/scratch/stefan/7769659/working/3D/220' -> `0.mol2'
Preparing input files

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

`REAL300000078188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078188 none COC1=CC=CC(NN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 28, 28, 28, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 7, 21, 30, 41, 56, 56, 1, 28, 36, 36, 36, 28, 28, 28, 18, 9, 9, 9, 1, 1, 1, 21, 21, 30, 30, 41, 41, 1, 28] 201
rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45])
total number of confs: 312
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078188 none COC1=CC=CC(NN=C(C)C2=CC=CC(OCCCC(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 6, 7, 28, 28, 28, 28, 28, 93, 141, 152, 185, 201, 201, 28, 1, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 28, 28, 28, 141, 141, 152, 152, 185, 185, 28, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 45, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 680
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078188 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078188
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078188/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078188
Building REAL300000078189
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078189'
/scratch/stefan/7769659/working/building/REAL300000078189 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078189

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078189/0 /scratch/stefan/7769659/working/building/REAL300000078189 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/221
`/scratch/stefan/7769659/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=C1)

`REAL300000078189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078189 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OC(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.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 43, 43, 43, 43, 43, 18, 18, 5, 2, 5, 2, 1, 1, 1, 1, 1, 1, 10, 24, 24, 31, 31, 1, 1, 43, 63, 63, 63, 43, 43, 43, 5, 5, 5, 5, 2, 2, 2, 2, 1, 1, 24, 24, 24, 24, 1, 1, 43] 201
rigid atoms, others: [40, 41, 12, 13, 14, 15, 16, 17, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 48])
total number of confs: 212
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078189 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OC(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.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 43, 43, 43, 43, 43, 43, 140, 195, 195, 201, 201, 43, 43, 1, 3, 3, 3, 1, 1, 1, 24, 24, 24, 24, 43, 43, 43, 43, 43, 43, 195, 195, 195, 195, 43, 43, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 48, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 622
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078189 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078189
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078189/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078189
Building REAL300000078190
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078190'
/scratch/stefan/7769659/working/building/REAL300000078190 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078190

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078190/0 /scratch/stefan/7769659/working/building/REAL300000078190 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/222
`/scratch/stefan/7769659/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=C1)

`REAL300000078190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078190 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 44, 44, 44, 44, 20, 20, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 6, 19, 32, 32, 1, 1, 44, 61, 61, 61, 44, 44, 44, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 19, 19, 1, 1, 44] 201
rigid atoms, others: [39, 40, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45])
total number of confs: 206
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078190 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 44, 44, 44, 44, 44, 44, 137, 186, 201, 201, 44, 44, 1, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 44, 44, 44, 44, 44, 44, 186, 186, 44, 44, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 45, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 616
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078190 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078190
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078190/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078190
Building REAL300000078191
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078191'
/scratch/stefan/7769659/working/building/REAL300000078191 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078191

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078191/0 /scratch/stefan/7769659/working/building/REAL300000078191 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/223
`/scratch/stefan/7769659/working/3D/223' -> `0.mol2'
Preparing input files

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

`REAL300000078191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078191 none COC1=CC=CC(NN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 55, 55, 55, 55, 55, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 22, 22, 30, 30, 1, 55, 74, 74, 74, 55, 55, 55, 21, 9, 9, 9, 1, 1, 1, 22, 22, 22, 22, 1, 55] 201
rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 42])
total number of confs: 235
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078191 none COC1=CC=CC(NN=C(C)C2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 24, 23, 24, 55, 55, 55, 55, 55, 150, 194, 194, 200, 200, 55, 1, 3, 3, 3, 1, 1, 1, 7, 24, 24, 24, 55, 55, 55, 194, 194, 194, 194, 55, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 485
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078191 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078191
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078191/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078191
Building REAL300000078192
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078192'
/scratch/stefan/7769659/working/building/REAL300000078192 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078192

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078192/0 /scratch/stefan/7769659/working/building/REAL300000078192 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/224
`/scratch/stefan/7769659/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=C1)

`REAL300000078192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078192 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 42, 42, 42, 42, 19, 19, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 16, 16, 1, 1, 42, 59, 59, 59, 42, 42, 42, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 42] 201
rigid atoms, others: [40, 41, 12, 13, 14, 15, 16, 17, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 48])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078192 none COC1=CC=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 42, 42, 42, 42, 42, 42, 155, 156, 156, 201, 201, 42, 42, 1, 3, 3, 3, 1, 1, 1, 26, 26, 26, 26, 42, 42, 42, 42, 42, 42, 156, 156, 156, 156, 42, 42, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 48, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 499
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078192 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078192
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078192/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078192
Building REAL300000078193
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078193'
/scratch/stefan/7769659/working/building/REAL300000078193 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078193

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078193/0 /scratch/stefan/7769659/working/building/REAL300000078193 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/225
`/scratch/stefan/7769659/working/3D/225' -> `0.mol2'
Preparing input files

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

`REAL300000078193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078193 none CCC(=NNC1=CC=CC(OC)=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 1, 7, 7, 20, 28, 28, 28, 28, 28, 36, 28, 1, 1, 1, 1, 1, 6, 10, 23, 23, 33, 35, 39, 1, 1, 11, 11, 11, 11, 11, 20, 28, 28, 28, 36, 36, 36, 28, 1, 1, 10, 10, 22, 22, 23, 23, 32, 32, 1, 1] 201
rigid atoms, others: [2, 40, 41, 13, 14, 15, 16, 17, 50, 51, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 271
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078193 none CCC(=NNC1=CC=CC(OC)=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 8, 28, 28, 9, 18, 89, 96, 132, 132, 160, 183, 187, 28, 28, 13, 13, 13, 13, 13, 2, 1, 1, 1, 2, 2, 2, 1, 28, 28, 96, 96, 132, 132, 132, 132, 160, 160, 28, 28] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 685
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078193 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078193
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078193/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078193
Building REAL300000078194
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078194'
/scratch/stefan/7769659/working/building/REAL300000078194 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078194

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078194/0 /scratch/stefan/7769659/working/building/REAL300000078194 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/226
`/scratch/stefan/7769659/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1)

`REAL300000078194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078194 none COC1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [70, 47, 47, 47, 47, 47, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 2, 7, 7, 1, 47, 70, 70, 70, 47, 47, 47, 1, 1, 1, 7, 7, 3, 7, 7, 1, 1, 47] 111
rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 15, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 39])
total number of confs: 131
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078194 none COC1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 9, 9, 47, 47, 47, 66, 66, 47, 91, 91, 49, 91, 91, 47, 1, 3, 3, 3, 1, 1, 1, 47, 47, 47, 91, 91, 63, 91, 91, 47, 47, 1] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 22, 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, 36, 37, 38])
total number of confs: 356
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078194 none COC1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [111, 91, 91, 91, 91, 91, 49, 49, 7, 7, 7, 1, 7, 10, 10, 1, 1, 1, 1, 1, 1, 7, 91, 111, 111, 111, 91, 91, 91, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 91] 111
rigid atoms, others: [32, 33, 34, 35, 36, 11, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 186
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078194 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078194
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078194/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078194
Building REAL300000078195
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078195'
/scratch/stefan/7769659/working/building/REAL300000078195 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078195

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078195/0 /scratch/stefan/7769659/working/building/REAL300000078195 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/227
`/scratch/stefan/7769659/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=C1)

`REAL300000078195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078195 none COC1=CC=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [98, 69, 69, 69, 69, 69, 25, 25, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 14, 14, 1, 1, 1, 69, 98, 98, 98, 69, 69, 69, 4, 4, 4, 4, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2, 69] 138
rigid atoms, others: [34, 35, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078195 none COC1=CC=CC(N=NC(C)[C@@H]2C[C@H](CC(=O)[O-])C2(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 42, 69, 69, 69, 69, 69, 111, 124, 124, 69, 69, 69, 1, 3, 3, 3, 1, 1, 1, 42, 42, 42, 42, 69, 69, 111, 111, 69, 69, 69, 69, 69, 69, 1] 138
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 44, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078195 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078195
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078195/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078195
Building REAL300000078196
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078196'
/scratch/stefan/7769659/working/building/REAL300000078196 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078196

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078196/0 /scratch/stefan/7769659/working/building/REAL300000078196 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/228
`/scratch/stefan/7769659/working/3D/228' -> `0.mol2'
Preparing input files

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

`REAL300000078196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078196 none COC1=CC=CC(NN=C(C)C2=CC=C(OCCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 42, 42, 42, 42, 42, 23, 11, 11, 1, 11, 1, 1, 1, 1, 1, 8, 20, 22, 31, 38, 38, 1, 1, 3, 1, 42, 53, 53, 53, 42, 42, 42, 23, 11, 11, 11, 1, 1, 20, 20, 22, 22, 31, 31, 3, 3, 3, 1, 42] 201
rigid atoms, others: [37, 38, 9, 11, 12, 13, 14, 15, 48, 22, 23, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49])
total number of confs: 275
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078196 none COC1=CC=CC(NN=C(C)C2=CC=C(OCCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 8, 7, 8, 42, 42, 42, 42, 96, 168, 172, 194, 194, 194, 42, 42, 66, 42, 1, 3, 3, 3, 1, 1, 1, 4, 8, 8, 8, 42, 42, 168, 168, 172, 172, 194, 194, 66, 66, 66, 42, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 49, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 691
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078196 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078196
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078196/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078196
Building REAL300000078197
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078197'
/scratch/stefan/7769659/working/building/REAL300000078197 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078197

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078197/0 /scratch/stefan/7769659/working/building/REAL300000078197 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/229
`/scratch/stefan/7769659/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=C(C)C2=CC(Br)=CC=C2OCC(=O)[O-])=C1)

`REAL300000078197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078197 none COC1=CC=CC(NN=C(C)C2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 60, 60, 60, 60, 60, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 54, 54, 60, 83, 83, 83, 60, 60, 60, 19, 6, 6, 6, 1, 1, 1, 31, 31, 60] 201
rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39])
total number of confs: 322
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078197 none COC1=CC=CC(NN=C(C)C2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 60, 60, 60, 60, 60, 60, 60, 127, 189, 201, 201, 1, 3, 3, 3, 1, 1, 1, 7, 26, 26, 26, 60, 60, 60, 189, 189, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078197 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078197
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078197/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078197
Building REAL300000078198
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078198'
/scratch/stefan/7769659/working/building/REAL300000078198 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078198 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `/scratch/stefan/7769659/failed'
`/scratch/stefan/7769659/working/building/REAL300000078198' -> `/scratch/stefan/7769659/failed/REAL300000078198'
Building REAL300000078199
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078199'
/scratch/stefan/7769659/working/building/REAL300000078199 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078199

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078199/0 /scratch/stefan/7769659/working/building/REAL300000078199 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/230
`/scratch/stefan/7769659/working/3D/230' -> `0.mol2'
Preparing input files

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

`REAL300000078199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078199 none COC1=CC=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 47, 47, 47, 47, 47, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 47, 67, 67, 67, 47, 47, 47, 26, 8, 1, 1, 1, 47] 67
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 16, 17, 20, 21, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078199 none COC1=CC=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 13, 39, 39, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 3, 3, 3, 1, 1, 1, 13, 39, 47, 47, 47, 1] 67
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078199 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078199
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078199/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078199
Building REAL300000078200
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078200'
/scratch/stefan/7769659/working/building/REAL300000078200 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078200

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078200/0 /scratch/stefan/7769659/working/building/REAL300000078200 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/231
`/scratch/stefan/7769659/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1)

`REAL300000078200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078200 none COC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 37, 36, 37, 37, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 26, 30, 30, 26, 31, 31, 26, 31, 31, 1, 37, 49, 49, 49, 36, 37, 37, 13, 6, 1, 1, 1, 26, 31, 31, 26, 31, 31, 1, 37] 201
rigid atoms, others: [45, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 46])
total number of confs: 211
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078200 none COC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 37, 37, 37, 37, 37, 105, 182, 190, 190, 182, 193, 193, 182, 193, 193, 37, 1, 3, 3, 3, 1, 1, 1, 7, 18, 37, 37, 37, 182, 193, 193, 182, 193, 193, 37, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 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, 42, 43, 44, 45])
total number of confs: 621
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078200 none COC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 193, 193, 193, 193, 118, 70, 70, 31, 31, 31, 31, 31, 7, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 31, 193, 201, 201, 201, 193, 193, 193, 118, 70, 31, 31, 31, 3, 1, 1, 1, 1, 1, 31, 193] 201
rigid atoms, others: [40, 41, 42, 43, 44, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46])
total number of confs: 476
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078200 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078200
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078200/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078200
Building REAL300000078201
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078201'
/scratch/stefan/7769659/working/building/REAL300000078201 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078201

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078201/0 /scratch/stefan/7769659/working/building/REAL300000078201 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/232
`/scratch/stefan/7769659/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1)

`REAL300000078201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078201 none COC1=CC=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 62, 62, 62, 62, 62, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 62, 71, 71, 71, 62, 62, 62, 31, 9, 1, 1, 1, 1, 1, 62] 71
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078201 none COC1=CC=CC(NN=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 1, 11, 43, 43, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 3, 3, 3, 1, 1, 1, 11, 43, 62, 62, 62, 62, 62, 1] 71
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: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078201 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078201
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078201/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078201
Building REAL300000078202
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078202'
/scratch/stefan/7769659/working/building/REAL300000078202 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078202

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078202/0 /scratch/stefan/7769659/working/building/REAL300000078202 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/233
`/scratch/stefan/7769659/working/3D/233' -> `0.mol2'
Preparing input files

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

`REAL300000078202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078202 none COC1=CC=CC(NN=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 59, 59, 59, 59, 59, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 18, 18, 1, 1, 3, 1, 59, 90, 90, 90, 59, 59, 59, 16, 6, 1, 13, 14, 14, 14, 4, 4, 4, 1, 59] 201
rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 43])
total number of confs: 238
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078202 none COC1=CC=CC(NN=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 59, 59, 59, 59, 59, 128, 180, 180, 198, 198, 59, 59, 106, 59, 1, 2, 2, 2, 1, 1, 1, 7, 21, 59, 180, 180, 180, 180, 106, 106, 106, 59, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 43, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078202 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078202
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078202/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078202
Building REAL300000078203
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078203'
/scratch/stefan/7769659/working/building/REAL300000078203 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078203

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078203/0 /scratch/stefan/7769659/working/building/REAL300000078203 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/234
`/scratch/stefan/7769659/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1)

`REAL300000078203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078203 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [170, 113, 113, 113, 113, 113, 51, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 113, 170, 170, 170, 113, 113, 113, 51, 11, 1, 113] 170
rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078203 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 13, 51, 51, 113, 113, 113, 135, 135, 113, 113, 113, 1, 2, 2, 2, 1, 1, 1, 13, 51, 113, 1] 170
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 23, 24, 25, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078203 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078203
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078203/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078203
Building REAL300000078204
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078204'
/scratch/stefan/7769659/working/building/REAL300000078204 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078204

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078204/0 /scratch/stefan/7769659/working/building/REAL300000078204 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/235
`/scratch/stefan/7769659/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1)

`REAL300000078204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078204 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [117, 80, 80, 80, 80, 80, 27, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 12, 12, 13, 13, 13, 13, 13, 1, 80, 117, 117, 117, 80, 80, 80, 26, 6, 1, 1, 13, 13, 26, 13, 80] 402
rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078204 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 1, 1, 1, 1, 1, 1, 11, 42, 42, 80, 80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 1, 3, 3, 3, 1, 1, 1, 11, 42, 80, 80, 201, 201, 402, 201, 1] 402
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 694
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078204 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 116, 47, 47, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 201, 201, 201, 201, 201, 201, 201, 116, 47, 13, 13, 1, 1, 2, 1, 201] 402
rigid atoms, others: [36, 37, 39, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 40])
total number of confs: 442
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078204 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078204
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078204/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078204
Building REAL300000078205
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078205'
/scratch/stefan/7769659/working/building/REAL300000078205 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078205

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078205/0 /scratch/stefan/7769659/working/building/REAL300000078205 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/236
`/scratch/stefan/7769659/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=C1)

`REAL300000078205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078205 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 33, 33, 33, 33, 33, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 33, 38, 38, 38, 33, 33, 33, 18, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 33] 38
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078205 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2N(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 11, 28, 28, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 3, 3, 3, 1, 1, 1, 11, 28, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 38
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 22, 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, 36, 37, 38, 39])
total number of confs: 61
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078205 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078205
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078205/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078205
Building REAL300000078206
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078206'
/scratch/stefan/7769659/working/building/REAL300000078206 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078206

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078206/0 /scratch/stefan/7769659/working/building/REAL300000078206 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/237
`/scratch/stefan/7769659/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1)

`REAL300000078206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078206 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [107, 71, 71, 71, 71, 71, 25, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 71, 107, 107, 107, 71, 71, 71, 24, 6, 1, 1, 12, 12, 12, 12, 71] 201
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078206 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 71, 71, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 71, 1, 2, 2, 2, 1, 1, 1, 9, 36, 71, 71, 201, 201, 201, 201, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078206 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 201, 201, 119, 52, 52, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 119, 52, 12, 12, 1, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 432
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078206 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078206
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078206/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078206
Building REAL300000078207
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078207'
/scratch/stefan/7769659/working/building/REAL300000078207 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078207

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078207/0 /scratch/stefan/7769659/working/building/REAL300000078207 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/238
`/scratch/stefan/7769659/working/3D/238' -> `0.mol2'
Preparing input files

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

`REAL300000078207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078207 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [139, 112, 112, 111, 112, 112, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 112, 139, 139, 139, 111, 112, 112, 48, 12, 1, 1, 1, 3, 3, 3, 112] 141
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 275
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078207 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 48, 48, 112, 112, 112, 112, 112, 112, 112, 112, 112, 131, 1, 2, 2, 2, 1, 1, 1, 11, 48, 112, 112, 112, 131, 131, 131, 1] 141
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 199
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078207 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078207
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078207/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078207
Building REAL300000078208
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078208'
/scratch/stefan/7769659/working/building/REAL300000078208 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078208

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078208/0 /scratch/stefan/7769659/working/building/REAL300000078208 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/239
`/scratch/stefan/7769659/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1)

`REAL300000078208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078208 none COC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 53, 53, 53, 53, 53, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 62, 62, 62, 53, 53, 53, 26, 8, 1, 1, 1, 1, 53] 62
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078208 none COC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 9, 33, 33, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 2, 2, 2, 1, 1, 1, 9, 33, 53, 53, 53, 53, 1] 62
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 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])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078208 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078208
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078208/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078208
Building REAL300000078209
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078209'
/scratch/stefan/7769659/working/building/REAL300000078209 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078209

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078209/0 /scratch/stefan/7769659/working/building/REAL300000078209 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/240
`/scratch/stefan/7769659/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1)

`REAL300000078209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078209 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 70, 70, 70, 70, 70, 43, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 70, 87, 87, 87, 70, 70, 70, 43, 12, 1, 1, 1, 70] 87
rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078209 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 3, 3, 3, 1, 1, 1, 11, 36, 70, 70, 70, 1] 87
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078209 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078209
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078209/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078209
Building REAL300000078210
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078210'
/scratch/stefan/7769659/working/building/REAL300000078210 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078210

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078210/0 /scratch/stefan/7769659/working/building/REAL300000078210 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/241
`/scratch/stefan/7769659/working/3D/241' -> `0.mol2'
Preparing input files

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

`REAL300000078210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078210 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [153, 92, 92, 91, 92, 92, 26, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 92, 153, 153, 153, 91, 92, 92, 26, 6, 1, 1, 4, 4, 4, 1, 92] 175
rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 17, 18, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078210 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 92, 92, 92, 92, 122, 122, 92, 92, 117, 92, 1, 2, 2, 2, 1, 1, 1, 11, 37, 92, 92, 117, 117, 117, 92, 1] 175
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078210 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078210
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078210/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078210
Building REAL300000078211
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078211'
/scratch/stefan/7769659/working/building/REAL300000078211 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078211

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078211/0 /scratch/stefan/7769659/working/building/REAL300000078211 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/242
`/scratch/stefan/7769659/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1)

`REAL300000078211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078211 none COC1=CC=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 57, 57, 56, 57, 57, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 62, 62, 62, 56, 57, 57, 31, 6, 1, 1, 57] 62
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078211 none COC1=CC=CC(NN=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 39, 39, 57, 57, 57, 39, 42, 57, 57, 57, 57, 57, 1, 3, 3, 3, 1, 1, 1, 11, 39, 57, 57, 1] 62
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078211 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078211
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078211/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078211
Building REAL300000078212
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078212'
/scratch/stefan/7769659/working/building/REAL300000078212 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078212

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078212/0 /scratch/stefan/7769659/working/building/REAL300000078212 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/243
`/scratch/stefan/7769659/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1)

`REAL300000078212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078212 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [63, 55, 55, 55, 55, 55, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 63, 63, 63, 55, 55, 55, 26, 10, 1, 1, 2, 55] 126
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 128
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078212 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 3, 3, 3, 1, 1, 1, 11, 35, 55, 55, 110, 1] 126
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 203
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078212 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078212/1 /scratch/stefan/7769659/working/building/REAL300000078212 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/244
`/scratch/stefan/7769659/working/3D/244' -> `1.mol2'
Preparing input files

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

`REAL300000078212.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078212/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078212 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 23, 23, 23, 23, 23, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 23, 23, 23, 14, 4, 1, 1, 23] 24
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078212 none COC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 11, 19, 19, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 1, 1, 1, 11, 19, 23, 23, 1] 24
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078212 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078212
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078212/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078212/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078212
Building REAL300000078213
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078213'
/scratch/stefan/7769659/working/building/REAL300000078213 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078213

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078213/0 /scratch/stefan/7769659/working/building/REAL300000078213 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/245
`/scratch/stefan/7769659/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1)

`REAL300000078213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078213 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 61, 61, 61, 61, 61, 20, 6, 6, 1, 1, 1, 1, 1, 1, 2, 6, 23, 23, 23, 23, 23, 23, 23, 1, 1, 61, 93, 93, 93, 61, 61, 61, 20, 6, 1, 1, 6, 6, 23, 23, 1, 1, 61] 201
rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43])
total number of confs: 210
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078213 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 61, 61, 35, 47, 97, 107, 201, 201, 201, 201, 201, 201, 201, 61, 61, 1, 3, 3, 3, 1, 1, 1, 8, 34, 61, 61, 107, 107, 201, 201, 61, 61, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 468
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078213 none COC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 114, 52, 52, 23, 23, 23, 23, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 201, 201, 114, 52, 22, 23, 9, 9, 1, 1, 23, 23, 201] 201
rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43])
total number of confs: 452
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078213 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078213
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078213/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078213
Building REAL300000078214
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078214'
/scratch/stefan/7769659/working/building/REAL300000078214 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078214

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078214/0 /scratch/stefan/7769659/working/building/REAL300000078214 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/246
`/scratch/stefan/7769659/working/3D/246' -> `0.mol2'
Preparing input files

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

`REAL300000078214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078214 none COC1=CC=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 54, 54, 54, 54, 54, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 66, 66, 66, 54, 54, 54, 27, 9, 1, 1, 1, 54] 66
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078214 none COC1=CC=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 10, 40, 40, 54, 54, 54, 53, 54, 54, 54, 54, 54, 1, 3, 3, 3, 1, 1, 1, 10, 40, 54, 53, 54, 1] 66
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 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
/scratch/stefan/7769659/working/building/REAL300000078214 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078214
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078214/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078214
Building REAL300000078215
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078215'
/scratch/stefan/7769659/working/building/REAL300000078215 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078215

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078215/0 /scratch/stefan/7769659/working/building/REAL300000078215 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/247
`/scratch/stefan/7769659/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1)

`REAL300000078215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078215 none COC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
204  conformations in input
total number of sets (complete confs): 204
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 102, 102, 102, 40, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 40, 11, 2, 1, 1, 1, 1, 1, 102] 204
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39])
total number of confs: 190
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078215 none COC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
204  conformations in input
total number of sets (complete confs): 204
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 3, 3, 3, 1, 1, 1, 11, 46, 204, 102, 102, 102, 102, 102, 1] 204
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 371
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078215 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078215
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078215/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078215
Building REAL300000078216
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078216'
/scratch/stefan/7769659/working/building/REAL300000078216 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078216

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078216/0 /scratch/stefan/7769659/working/building/REAL300000078216 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/248
`/scratch/stefan/7769659/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1)

`REAL300000078216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078216 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [69, 59, 59, 59, 59, 59, 19, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 9, 25, 25, 5, 1, 1, 59, 69, 69, 69, 59, 59, 59, 18, 5, 1, 1, 5, 5, 2, 9, 9, 5, 1, 1, 59] 201
rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 43, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 206
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078216 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 1, 10, 36, 36, 59, 59, 36, 36, 125, 125, 36, 125, 125, 186, 198, 198, 125, 59, 59, 1, 3, 3, 3, 1, 1, 1, 10, 36, 59, 59, 125, 125, 52, 186, 186, 125, 59, 59, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 45, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 866
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078216 none COC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [138, 125, 125, 125, 125, 125, 47, 11, 11, 1, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 125, 138, 138, 138, 125, 125, 125, 46, 11, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 125] 201
rigid atoms, others: [37, 38, 39, 42, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 43, 44, 45])
total number of confs: 284
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078216 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078216
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078216/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078216
Building REAL300000078217
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078217'
/scratch/stefan/7769659/working/building/REAL300000078217 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078217

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078217/0 /scratch/stefan/7769659/working/building/REAL300000078217 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/249
`/scratch/stefan/7769659/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC=CC(OC)=C2)=CC=C1OCC(=O)[O-])

`REAL300000078217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078217 none CCOC1=CC(C=NNC2=CC=CC(OC)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 58, 27, 26, 26, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 27, 26, 26, 26, 93, 176, 189, 189, 74, 74, 74, 74, 74, 27, 8, 4, 1, 1, 1, 3, 3, 3, 1, 27, 27, 176, 176] 201
rigid atoms, others: [33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078217 none CCOC1=CC(C=NNC2=CC=CC(OC)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 1, 1, 1, 1, 1, 6, 6, 13, 27, 27, 27, 27, 27, 37, 27, 1, 1, 1, 1, 7, 33, 55, 55, 16, 16, 16, 16, 16, 1, 6, 12, 27, 27, 27, 37, 37, 37, 26, 1, 1, 33, 33] 201
rigid atoms, others: [2, 3, 4, 5, 6, 40, 41, 17, 18, 19, 20, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078217 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078217
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078217/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078217
Building REAL300000078218
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078218'
/scratch/stefan/7769659/working/building/REAL300000078218 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078218

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078218/0 /scratch/stefan/7769659/working/building/REAL300000078218 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/250
`/scratch/stefan/7769659/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1)

`REAL300000078218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078218 none COC1=CC=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 85, 85, 85, 85, 85, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 85, 94, 94, 94, 85, 85, 85, 36, 9, 1, 1, 1, 1, 1, 85] 94
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078218 none COC1=CC=CC(NN=CC2=CNC3=C(C(=O)[O-])C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 1, 1, 1, 1, 1, 1, 11, 48, 48, 85, 85, 85, 85, 85, 88, 88, 85, 85, 85, 85, 1, 3, 3, 3, 1, 1, 1, 11, 48, 85, 85, 85, 85, 85, 1] 94
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: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078218 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078218
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078218/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078218
Building REAL300000078219
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078219'
/scratch/stefan/7769659/working/building/REAL300000078219 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078219

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078219/0 /scratch/stefan/7769659/working/building/REAL300000078219 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/251
`/scratch/stefan/7769659/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1)

`REAL300000078219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078219 none COC1=CC=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 86, 86, 86, 86, 86, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 86, 97, 97, 97, 86, 86, 86, 38, 8, 1, 1, 1, 1, 86] 97
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078219 none COC1=CC=CC(NN=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 39, 39, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 2, 2, 2, 1, 1, 1, 11, 39, 86, 86, 86, 86, 1] 97
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 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])
total number of confs: 138
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078219 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078219
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078219/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078219
Building REAL300000078220
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078220'
/scratch/stefan/7769659/working/building/REAL300000078220 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078220

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078220/0 /scratch/stefan/7769659/working/building/REAL300000078220 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/252
`/scratch/stefan/7769659/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1)

`REAL300000078220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078220 none COC1=CC=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 58, 57, 58, 58, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 63, 63, 63, 57, 58, 58, 28, 6, 1, 1, 1, 1, 58] 63
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078220 none COC1=CC=CC(NN=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 13, 43, 43, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 3, 3, 3, 1, 1, 1, 13, 43, 58, 58, 58, 58, 1] 63
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 22, 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])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078220 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078220
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078220/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078220
Building REAL300000078221
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078221'
/scratch/stefan/7769659/working/building/REAL300000078221 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078221

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078221/0 /scratch/stefan/7769659/working/building/REAL300000078221 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/253
`/scratch/stefan/7769659/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1)

`REAL300000078221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078221 none COC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 20, 20, 20, 20, 20, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 82, 82, 82, 82, 82, 82, 82, 20, 25, 25, 25, 20, 20, 20, 8, 4, 1, 1, 1, 1, 27, 27, 82, 82, 20] 201
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078221 none COC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 20, 20, 14, 20, 20, 20, 52, 117, 201, 201, 201, 201, 201, 201, 201, 1, 3, 3, 3, 1, 1, 1, 7, 14, 20, 20, 20, 20, 117, 117, 201, 201, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 523
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078221 none COC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 127, 94, 94, 82, 82, 82, 82, 82, 82, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 127, 94, 82, 82, 82, 82, 9, 9, 1, 1, 201] 201
rigid atoms, others: [41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43])
total number of confs: 443
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078221 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078221
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078221/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078221
Building REAL300000078222
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078222'
/scratch/stefan/7769659/working/building/REAL300000078222 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078222

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078222/0 /scratch/stefan/7769659/working/building/REAL300000078222 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/254
`/scratch/stefan/7769659/working/3D/254' -> `0.mol2'
Preparing input files

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

`REAL300000078222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078222 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 54, 54, 54, 54, 54, 19, 7, 7, 1, 1, 1, 1, 1, 1, 7, 31, 53, 53, 1, 1, 1, 54, 82, 82, 82, 54, 54, 54, 19, 7, 1, 1, 31, 31, 1, 54] 201
rigid atoms, others: [32, 35, 9, 10, 11, 12, 13, 14, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 329
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078222 none COC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 53, 54, 33, 54, 135, 189, 192, 192, 54, 54, 54, 1, 3, 3, 3, 1, 1, 1, 7, 23, 54, 54, 189, 189, 54, 1] 201
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: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078222 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078222
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078222/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078222
Building REAL300000078223
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078223'
/scratch/stefan/7769659/working/building/REAL300000078223 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078223

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078223/0 /scratch/stefan/7769659/working/building/REAL300000078223 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/255
`/scratch/stefan/7769659/working/3D/255' -> `0.mol2'
Preparing input files

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

`REAL300000078223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078223 none COC1=CC=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 28, 28, 28, 28, 28, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 28, 44, 44, 44, 28, 28, 28, 8, 4, 1, 1, 9, 17, 17, 1, 1, 28] 139
rigid atoms, others: [33, 34, 38, 39, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40])
total number of confs: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078223 none COC1=CC=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 28, 28, 15, 15, 50, 50, 50, 113, 139, 139, 139, 28, 28, 1, 3, 3, 3, 1, 1, 1, 6, 14, 28, 28, 113, 139, 139, 28, 28, 1] 139
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 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
/scratch/stefan/7769659/working/building/REAL300000078223 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078223
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078223/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078223
Building REAL300000078224
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078224'
/scratch/stefan/7769659/working/building/REAL300000078224 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078224

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078224/0 /scratch/stefan/7769659/working/building/REAL300000078224 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/256
`/scratch/stefan/7769659/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1)

`REAL300000078224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078224 none COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 109, 109, 108, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 47, 12, 1, 1, 1, 109] 109
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078224 none COC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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
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, 1, 11, 49, 49, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 1, 2, 2, 2, 1, 1, 1, 11, 49, 109, 109, 109, 1] 109
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078224 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078224
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078224/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078224
Building REAL300000078225
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078225'
/scratch/stefan/7769659/working/building/REAL300000078225 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078225

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078225/0 /scratch/stefan/7769659/working/building/REAL300000078225 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/257
`/scratch/stefan/7769659/working/3D/257' -> `0.mol2'
Preparing input files

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

`REAL300000078225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078225 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 69, 69, 68, 69, 69, 26, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 69, 96, 96, 96, 68, 69, 69, 26, 7, 1, 1, 1, 4, 4, 4, 69] 96
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078225 none COC1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 69, 69, 69, 69, 69, 69, 69, 69, 69, 83, 1, 3, 3, 3, 1, 1, 1, 11, 49, 69, 69, 69, 83, 83, 83, 1] 96
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078225 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078225
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078225/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078225
Building REAL300000078226
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078226'
/scratch/stefan/7769659/working/building/REAL300000078226 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078226

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078226/0 /scratch/stefan/7769659/working/building/REAL300000078226 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/258
`/scratch/stefan/7769659/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1)

`REAL300000078226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078226 none COC1=CC=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [93, 58, 58, 58, 58, 58, 14, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 12, 1, 1, 58, 93, 93, 93, 58, 58, 58, 14, 4, 12, 12, 12, 12, 1, 1, 58] 201
rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078226 none COC1=CC=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 58, 58, 58, 161, 161, 161, 161, 161, 179, 179, 161, 58, 58, 1, 3, 3, 3, 1, 1, 1, 9, 37, 161, 161, 161, 161, 58, 58, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 460
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078226 none COC1=CC=CC(NN=CC2=NN([C@H]3C[C@H](C(=O)[O-])C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 161, 161, 161, 161, 161, 75, 30, 30, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 161, 201, 201, 201, 161, 161, 161, 75, 30, 1, 1, 1, 1, 12, 12, 161] 201
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 406
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078226 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078226
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078226/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078226
Building REAL300000078227
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078227'
/scratch/stefan/7769659/working/building/REAL300000078227 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078227 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078227' -> `/scratch/stefan/7769659/failed/REAL300000078227'
Building REAL300000078228
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078228'
/scratch/stefan/7769659/working/building/REAL300000078228 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078228 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078228' -> `/scratch/stefan/7769659/failed/REAL300000078228'
Building REAL300000078229
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078229'
/scratch/stefan/7769659/working/building/REAL300000078229 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078229 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078229' -> `/scratch/stefan/7769659/failed/REAL300000078229'
Building REAL300000078230
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078230'
/scratch/stefan/7769659/working/building/REAL300000078230 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078230 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078230' -> `/scratch/stefan/7769659/failed/REAL300000078230'
Building REAL300000078231
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078231'
/scratch/stefan/7769659/working/building/REAL300000078231 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078231 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078231' -> `/scratch/stefan/7769659/failed/REAL300000078231'
Building REAL300000078232
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078232'
/scratch/stefan/7769659/working/building/REAL300000078232 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078232 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078232' -> `/scratch/stefan/7769659/failed/REAL300000078232'
Building REAL300000078233
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078233'
/scratch/stefan/7769659/working/building/REAL300000078233 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078233 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078233' -> `/scratch/stefan/7769659/failed/REAL300000078233'
Building REAL300000078234
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078234'
/scratch/stefan/7769659/working/building/REAL300000078234 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078234 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078234' -> `/scratch/stefan/7769659/failed/REAL300000078234'
Building REAL300000078235
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078235'
/scratch/stefan/7769659/working/building/REAL300000078235 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078235 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078235' -> `/scratch/stefan/7769659/failed/REAL300000078235'
Building REAL300000078236
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078236'
/scratch/stefan/7769659/working/building/REAL300000078236 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078236 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078236' -> `/scratch/stefan/7769659/failed/REAL300000078236'
Building REAL300000078237
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078237'
/scratch/stefan/7769659/working/building/REAL300000078237 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078237 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078237' -> `/scratch/stefan/7769659/failed/REAL300000078237'
Building REAL300000078238
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078238'
/scratch/stefan/7769659/working/building/REAL300000078238 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078238 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078238' -> `/scratch/stefan/7769659/failed/REAL300000078238'
Building REAL300000078239
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078239'
/scratch/stefan/7769659/working/building/REAL300000078239 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078239 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078239' -> `/scratch/stefan/7769659/failed/REAL300000078239'
Building REAL300000078240
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078240'
/scratch/stefan/7769659/working/building/REAL300000078240 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078240 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078240' -> `/scratch/stefan/7769659/failed/REAL300000078240'
Building REAL300000078241
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078241'
/scratch/stefan/7769659/working/building/REAL300000078241 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078241 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078241' -> `/scratch/stefan/7769659/failed/REAL300000078241'
Building REAL300000078242
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078242'
/scratch/stefan/7769659/working/building/REAL300000078242 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078242 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078242' -> `/scratch/stefan/7769659/failed/REAL300000078242'
Building REAL300000078243
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078243'
/scratch/stefan/7769659/working/building/REAL300000078243 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078243 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078243' -> `/scratch/stefan/7769659/failed/REAL300000078243'
Building REAL300000078244
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078244'
/scratch/stefan/7769659/working/building/REAL300000078244 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078244 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078244' -> `/scratch/stefan/7769659/failed/REAL300000078244'
Building REAL300000078245
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078245'
/scratch/stefan/7769659/working/building/REAL300000078245 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078245 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078245' -> `/scratch/stefan/7769659/failed/REAL300000078245'
Building REAL300000078246
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078246'
/scratch/stefan/7769659/working/building/REAL300000078246 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078246 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078246' -> `/scratch/stefan/7769659/failed/REAL300000078246'
Building REAL300000078247
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078247'
/scratch/stefan/7769659/working/building/REAL300000078247 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078247 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078247' -> `/scratch/stefan/7769659/failed/REAL300000078247'
Building REAL300000078248
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078248'
/scratch/stefan/7769659/working/building/REAL300000078248 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078248 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078248' -> `/scratch/stefan/7769659/failed/REAL300000078248'
Building REAL300000078249
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078249'
/scratch/stefan/7769659/working/building/REAL300000078249 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078249 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078249' -> `/scratch/stefan/7769659/failed/REAL300000078249'
Building REAL300000078250
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078250'
/scratch/stefan/7769659/working/building/REAL300000078250 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078250 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078250' -> `/scratch/stefan/7769659/failed/REAL300000078250'
Building REAL300000078251
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078251'
/scratch/stefan/7769659/working/building/REAL300000078251 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078251 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078251' -> `/scratch/stefan/7769659/failed/REAL300000078251'
Building REAL300000078252
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078252'
/scratch/stefan/7769659/working/building/REAL300000078252 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078252 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078252' -> `/scratch/stefan/7769659/failed/REAL300000078252'
Building REAL300000078253
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078253'
/scratch/stefan/7769659/working/building/REAL300000078253 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078253 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078253' -> `/scratch/stefan/7769659/failed/REAL300000078253'
Building REAL300000078254
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078254'
/scratch/stefan/7769659/working/building/REAL300000078254 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078254 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078254' -> `/scratch/stefan/7769659/failed/REAL300000078254'
Building REAL300000078255
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078255'
/scratch/stefan/7769659/working/building/REAL300000078255 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078255 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078255' -> `/scratch/stefan/7769659/failed/REAL300000078255'
Building REAL300000078256
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078256'
/scratch/stefan/7769659/working/building/REAL300000078256 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078256 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078256' -> `/scratch/stefan/7769659/failed/REAL300000078256'
Building REAL300000078257
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078257'
/scratch/stefan/7769659/working/building/REAL300000078257 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078257 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078257' -> `/scratch/stefan/7769659/failed/REAL300000078257'
Building REAL300000078258
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078258'
/scratch/stefan/7769659/working/building/REAL300000078258 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078258 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078258' -> `/scratch/stefan/7769659/failed/REAL300000078258'
Building REAL300000078259
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078259'
/scratch/stefan/7769659/working/building/REAL300000078259 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078259 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078259' -> `/scratch/stefan/7769659/failed/REAL300000078259'
Building REAL300000078260
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078260'
/scratch/stefan/7769659/working/building/REAL300000078260 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078260 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078260' -> `/scratch/stefan/7769659/failed/REAL300000078260'
Building REAL300000078261
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078261'
/scratch/stefan/7769659/working/building/REAL300000078261 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078261 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078261' -> `/scratch/stefan/7769659/failed/REAL300000078261'
Building REAL300000078262
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078262'
/scratch/stefan/7769659/working/building/REAL300000078262 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078262 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078262' -> `/scratch/stefan/7769659/failed/REAL300000078262'
Building REAL300000078263
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078263'
/scratch/stefan/7769659/working/building/REAL300000078263 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078263 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078263' -> `/scratch/stefan/7769659/failed/REAL300000078263'
Building REAL300000078264
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078264'
/scratch/stefan/7769659/working/building/REAL300000078264 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078264 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078264' -> `/scratch/stefan/7769659/failed/REAL300000078264'
Building REAL300000078265
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078265'
/scratch/stefan/7769659/working/building/REAL300000078265 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078265 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078265' -> `/scratch/stefan/7769659/failed/REAL300000078265'
Building REAL300000078266
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078266'
/scratch/stefan/7769659/working/building/REAL300000078266 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078266 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078266' -> `/scratch/stefan/7769659/failed/REAL300000078266'
Building REAL300000078267
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078267'
/scratch/stefan/7769659/working/building/REAL300000078267 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078267 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078267' -> `/scratch/stefan/7769659/failed/REAL300000078267'
Building REAL300000078268
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078268'
/scratch/stefan/7769659/working/building/REAL300000078268 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078268 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078268' -> `/scratch/stefan/7769659/failed/REAL300000078268'
Building REAL300000078269
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078269'
/scratch/stefan/7769659/working/building/REAL300000078269 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078269 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078269' -> `/scratch/stefan/7769659/failed/REAL300000078269'
Building REAL300000078270
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078270'
/scratch/stefan/7769659/working/building/REAL300000078270 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078270 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078270' -> `/scratch/stefan/7769659/failed/REAL300000078270'
Building REAL300000078271
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078271'
/scratch/stefan/7769659/working/building/REAL300000078271 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078271 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078271' -> `/scratch/stefan/7769659/failed/REAL300000078271'
Building REAL300000078272
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078272'
/scratch/stefan/7769659/working/building/REAL300000078272 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078272 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078272' -> `/scratch/stefan/7769659/failed/REAL300000078272'
Building REAL300000078273
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078273'
/scratch/stefan/7769659/working/building/REAL300000078273 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078273 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078273' -> `/scratch/stefan/7769659/failed/REAL300000078273'
Building REAL300000078274
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078274'
/scratch/stefan/7769659/working/building/REAL300000078274 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078274 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078274' -> `/scratch/stefan/7769659/failed/REAL300000078274'
Building REAL300000078275
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078275'
/scratch/stefan/7769659/working/building/REAL300000078275 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078275 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078275' -> `/scratch/stefan/7769659/failed/REAL300000078275'
Building REAL300000078276
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078276'
/scratch/stefan/7769659/working/building/REAL300000078276 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078276 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078276' -> `/scratch/stefan/7769659/failed/REAL300000078276'
Building REAL300000078277
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078277'
/scratch/stefan/7769659/working/building/REAL300000078277 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078277 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078277' -> `/scratch/stefan/7769659/failed/REAL300000078277'
Building REAL300000078278
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078278'
/scratch/stefan/7769659/working/building/REAL300000078278 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078278 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078278' -> `/scratch/stefan/7769659/failed/REAL300000078278'
Building REAL300000078279
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078279'
/scratch/stefan/7769659/working/building/REAL300000078279 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078279 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078279' -> `/scratch/stefan/7769659/failed/REAL300000078279'
Building REAL300000078280
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078280'
/scratch/stefan/7769659/working/building/REAL300000078280 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078280 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078280' -> `/scratch/stefan/7769659/failed/REAL300000078280'
Building REAL300000078281
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078281'
/scratch/stefan/7769659/working/building/REAL300000078281 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078281 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078281' -> `/scratch/stefan/7769659/failed/REAL300000078281'
Building REAL300000078282
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078282'
/scratch/stefan/7769659/working/building/REAL300000078282 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078282 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078282' -> `/scratch/stefan/7769659/failed/REAL300000078282'
Building REAL300000078283
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078283'
/scratch/stefan/7769659/working/building/REAL300000078283 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078283 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078283' -> `/scratch/stefan/7769659/failed/REAL300000078283'
Building REAL300000078284
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078284'
/scratch/stefan/7769659/working/building/REAL300000078284 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078284 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078284' -> `/scratch/stefan/7769659/failed/REAL300000078284'
Building REAL300000078285
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078285'
/scratch/stefan/7769659/working/building/REAL300000078285 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078285 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078285' -> `/scratch/stefan/7769659/failed/REAL300000078285'
Building REAL300000078286
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078286'
/scratch/stefan/7769659/working/building/REAL300000078286 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078286 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078286' -> `/scratch/stefan/7769659/failed/REAL300000078286'
Building REAL300000078287
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078287'
/scratch/stefan/7769659/working/building/REAL300000078287 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078287 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078287' -> `/scratch/stefan/7769659/failed/REAL300000078287'
Building REAL300000078288
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078288'
/scratch/stefan/7769659/working/building/REAL300000078288 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078288 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078288' -> `/scratch/stefan/7769659/failed/REAL300000078288'
Building REAL300000078289
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078289'
/scratch/stefan/7769659/working/building/REAL300000078289 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078289 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078289' -> `/scratch/stefan/7769659/failed/REAL300000078289'
Building REAL300000078290
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078290'
/scratch/stefan/7769659/working/building/REAL300000078290 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078290 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078290' -> `/scratch/stefan/7769659/failed/REAL300000078290'
Building REAL300000078291
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078291'
/scratch/stefan/7769659/working/building/REAL300000078291 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078291 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078291' -> `/scratch/stefan/7769659/failed/REAL300000078291'
Building REAL300000078292
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078292'
/scratch/stefan/7769659/working/building/REAL300000078292 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078292 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078292' -> `/scratch/stefan/7769659/failed/REAL300000078292'
Building REAL300000078293
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078293'
/scratch/stefan/7769659/working/building/REAL300000078293 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078293 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078293' -> `/scratch/stefan/7769659/failed/REAL300000078293'
Building REAL300000078294
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078294'
/scratch/stefan/7769659/working/building/REAL300000078294 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078294 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078294' -> `/scratch/stefan/7769659/failed/REAL300000078294'
Building REAL300000078295
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078295'
/scratch/stefan/7769659/working/building/REAL300000078295 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078295 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078295' -> `/scratch/stefan/7769659/failed/REAL300000078295'
Building REAL300000078296
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078296'
/scratch/stefan/7769659/working/building/REAL300000078296 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078296 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078296' -> `/scratch/stefan/7769659/failed/REAL300000078296'
Building REAL300000078297
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078297'
/scratch/stefan/7769659/working/building/REAL300000078297 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078297 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078297' -> `/scratch/stefan/7769659/failed/REAL300000078297'
Building REAL300000078298
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078298'
/scratch/stefan/7769659/working/building/REAL300000078298 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078298 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078298' -> `/scratch/stefan/7769659/failed/REAL300000078298'
Building REAL300000078299
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078299'
/scratch/stefan/7769659/working/building/REAL300000078299 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078299 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078299' -> `/scratch/stefan/7769659/failed/REAL300000078299'
Building REAL300000078300
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078300'
/scratch/stefan/7769659/working/building/REAL300000078300 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078300 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078300' -> `/scratch/stefan/7769659/failed/REAL300000078300'
Building REAL300000078301
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078301'
/scratch/stefan/7769659/working/building/REAL300000078301 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078301 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078301' -> `/scratch/stefan/7769659/failed/REAL300000078301'
Building REAL300000078302
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078302'
/scratch/stefan/7769659/working/building/REAL300000078302 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078302 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078302' -> `/scratch/stefan/7769659/failed/REAL300000078302'
Building REAL300000078303
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078303'
/scratch/stefan/7769659/working/building/REAL300000078303 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078303 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078303' -> `/scratch/stefan/7769659/failed/REAL300000078303'
Building REAL300000078304
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078304'
/scratch/stefan/7769659/working/building/REAL300000078304 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078304 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078304' -> `/scratch/stefan/7769659/failed/REAL300000078304'
Building REAL300000078305
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078305'
/scratch/stefan/7769659/working/building/REAL300000078305 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078305 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078305' -> `/scratch/stefan/7769659/failed/REAL300000078305'
Building REAL300000078306
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078306'
/scratch/stefan/7769659/working/building/REAL300000078306 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078306 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078306' -> `/scratch/stefan/7769659/failed/REAL300000078306'
Building REAL300000078307
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078307'
/scratch/stefan/7769659/working/building/REAL300000078307 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078307 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078307' -> `/scratch/stefan/7769659/failed/REAL300000078307'
Building REAL300000078308
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078308'
/scratch/stefan/7769659/working/building/REAL300000078308 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078308 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078308' -> `/scratch/stefan/7769659/failed/REAL300000078308'
Building REAL300000078309
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078309'
/scratch/stefan/7769659/working/building/REAL300000078309 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078309 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078309' -> `/scratch/stefan/7769659/failed/REAL300000078309'
Building REAL300000078310
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078310'
/scratch/stefan/7769659/working/building/REAL300000078310 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078310 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078310' -> `/scratch/stefan/7769659/failed/REAL300000078310'
Building REAL300000078311
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078311'
/scratch/stefan/7769659/working/building/REAL300000078311 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078311 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078311' -> `/scratch/stefan/7769659/failed/REAL300000078311'
Building REAL300000078312
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078312'
/scratch/stefan/7769659/working/building/REAL300000078312 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078312 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078312' -> `/scratch/stefan/7769659/failed/REAL300000078312'
Building REAL300000078313
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078313'
/scratch/stefan/7769659/working/building/REAL300000078313 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078313 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078313' -> `/scratch/stefan/7769659/failed/REAL300000078313'
Building REAL300000078314
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078314'
/scratch/stefan/7769659/working/building/REAL300000078314 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078314 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078314' -> `/scratch/stefan/7769659/failed/REAL300000078314'
Building REAL300000078315
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078315'
/scratch/stefan/7769659/working/building/REAL300000078315 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078315 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078315' -> `/scratch/stefan/7769659/failed/REAL300000078315'
Building REAL300000078316
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078316'
/scratch/stefan/7769659/working/building/REAL300000078316 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078316 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078316' -> `/scratch/stefan/7769659/failed/REAL300000078316'
Building REAL300000078317
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078317'
/scratch/stefan/7769659/working/building/REAL300000078317 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078317 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078317' -> `/scratch/stefan/7769659/failed/REAL300000078317'
Building REAL300000078318
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078318'
/scratch/stefan/7769659/working/building/REAL300000078318 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078318 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078318' -> `/scratch/stefan/7769659/failed/REAL300000078318'
Building REAL300000078319
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078319'
/scratch/stefan/7769659/working/building/REAL300000078319 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078319 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078319' -> `/scratch/stefan/7769659/failed/REAL300000078319'
Building REAL300000078320
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078320'
/scratch/stefan/7769659/working/building/REAL300000078320 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078320 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078320' -> `/scratch/stefan/7769659/failed/REAL300000078320'
Building REAL300000078321
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078321'
/scratch/stefan/7769659/working/building/REAL300000078321 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078321 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078321' -> `/scratch/stefan/7769659/failed/REAL300000078321'
Building REAL300000078322
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078322'
/scratch/stefan/7769659/working/building/REAL300000078322 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078322 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078322' -> `/scratch/stefan/7769659/failed/REAL300000078322'
Building REAL300000078323
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078323'
/scratch/stefan/7769659/working/building/REAL300000078323 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078323 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078323' -> `/scratch/stefan/7769659/failed/REAL300000078323'
Building REAL300000078324
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078324'
/scratch/stefan/7769659/working/building/REAL300000078324 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078324 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078324' -> `/scratch/stefan/7769659/failed/REAL300000078324'
Building REAL300000078325
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078325'
/scratch/stefan/7769659/working/building/REAL300000078325 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078325 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078325' -> `/scratch/stefan/7769659/failed/REAL300000078325'
Building REAL300000078326
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078326'
/scratch/stefan/7769659/working/building/REAL300000078326 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078326 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078326' -> `/scratch/stefan/7769659/failed/REAL300000078326'
Building REAL300000078327
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078327'
/scratch/stefan/7769659/working/building/REAL300000078327 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078327 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078327' -> `/scratch/stefan/7769659/failed/REAL300000078327'
Building REAL300000078328
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078328'
/scratch/stefan/7769659/working/building/REAL300000078328 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078328 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078328' -> `/scratch/stefan/7769659/failed/REAL300000078328'
Building REAL300000078329
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078329'
/scratch/stefan/7769659/working/building/REAL300000078329 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078329 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078329' -> `/scratch/stefan/7769659/failed/REAL300000078329'
Building REAL300000078330
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078330'
/scratch/stefan/7769659/working/building/REAL300000078330 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078330 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078330' -> `/scratch/stefan/7769659/failed/REAL300000078330'
Building REAL300000078331
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078331'
/scratch/stefan/7769659/working/building/REAL300000078331 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078331 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078331' -> `/scratch/stefan/7769659/failed/REAL300000078331'
Building REAL300000078332
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078332'
/scratch/stefan/7769659/working/building/REAL300000078332 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078332 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078332' -> `/scratch/stefan/7769659/failed/REAL300000078332'
Building REAL300000078333
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078333'
/scratch/stefan/7769659/working/building/REAL300000078333 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078333 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078333' -> `/scratch/stefan/7769659/failed/REAL300000078333'
Building REAL300000078334
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078334'
/scratch/stefan/7769659/working/building/REAL300000078334 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078334 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078334' -> `/scratch/stefan/7769659/failed/REAL300000078334'
Building REAL300000078335
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078335'
/scratch/stefan/7769659/working/building/REAL300000078335 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078335 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078335' -> `/scratch/stefan/7769659/failed/REAL300000078335'
Building REAL300000078336
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078336'
/scratch/stefan/7769659/working/building/REAL300000078336 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078336

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078336/0 /scratch/stefan/7769659/working/building/REAL300000078336 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/259
`/scratch/stefan/7769659/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078336 none CC(=NNC(=O)C1CCOC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 26, 56, 56, 56, 56, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 26, 56, 56, 56, 56, 56, 56, 56, 1, 1, 12, 12, 1, 1] 88
rigid atoms, others: [1, 36, 37, 40, 41, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 159
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078336 none CC(=NNC(=O)C1CCOC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 23, 56, 56, 23, 40, 88, 88, 88, 88, 88, 88, 88, 56, 56, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 56, 56, 88, 88, 56, 56] 88
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41])
total number of confs: 258
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078336 none CC(=NNC(=O)C1CCOC1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 12, 36, 36, 62, 62, 62, 88, 88, 88, 88, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 36, 36, 62, 88, 88, 88, 88, 88, 88, 88, 12, 12, 1, 1, 12, 12] 88
rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 289
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078336 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078336
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078336/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078336
Building REAL300000078337
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078337'
/scratch/stefan/7769659/working/building/REAL300000078337 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078337

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078337/0 /scratch/stefan/7769659/working/building/REAL300000078337 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/260
`/scratch/stefan/7769659/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-])

`REAL300000078337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078337 none COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 31, 31, 31, 12, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 31, 31, 31, 31, 125, 200, 201, 201, 58, 58, 58, 31, 12, 8, 1, 1, 1, 1, 1, 1, 1, 31, 31, 200, 200] 201
rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39])
total number of confs: 590
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078337 none COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 30, 31, 31, 31, 1, 1, 1, 1, 9, 41, 57, 57, 4, 4, 4, 1, 9, 17, 31, 31, 31, 31, 31, 31, 31, 1, 1, 41, 41] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 36, 26, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 286
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078337 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078337
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078337/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078337
Building REAL300000078338
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078338'
/scratch/stefan/7769659/working/building/REAL300000078338 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078338

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078338/0 /scratch/stefan/7769659/working/building/REAL300000078338 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/261
`/scratch/stefan/7769659/working/3D/261' -> `0.mol2'
Preparing input files

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

`REAL300000078338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078338 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 20, 20, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 7, 25, 38, 38, 1, 10, 10, 10, 20, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 25, 25, 1] 201
rigid atoms, others: [1, 34, 35, 38, 33, 11, 12, 13, 14, 15, 16, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 252
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078338 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 54, 54, 54, 54, 54, 124, 201, 201, 201, 54, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 201, 201, 54] 201
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38])
total number of confs: 559
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078338 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078338
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078338/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078338
Building REAL300000078339
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078339'
/scratch/stefan/7769659/working/building/REAL300000078339 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078339

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078339/0 /scratch/stefan/7769659/working/building/REAL300000078339 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/262
`/scratch/stefan/7769659/working/3D/262' -> `0.mol2'
Preparing input files

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

`REAL300000078339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078339 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 45, 45, 45, 45, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 11, 45, 45, 45, 45, 45, 45, 45, 1, 1, 9, 17, 17, 1, 1] 130
rigid atoms, others: [1, 36, 37, 41, 42, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 189
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078339 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 19, 45, 45, 19, 19, 75, 75, 75, 112, 130, 130, 130, 45, 45, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 45, 45, 112, 130, 130, 45, 45] 130
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 5, 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: 583
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078339 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078339
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078339/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078339
Building REAL300000078340
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078340'
/scratch/stefan/7769659/working/building/REAL300000078340 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078340

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078340/0 /scratch/stefan/7769659/working/building/REAL300000078340 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/263
`/scratch/stefan/7769659/working/3D/263' -> `0.mol2'
Preparing input files

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

`REAL300000078340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078340 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 1, 1, 9, 9, 9, 9, 9, 1, 1] 64
rigid atoms, others: [1, 45, 37, 38, 44, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 75
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078340 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 20, 20, 9, 9, 34, 34, 34, 64, 64, 64, 64, 64, 20, 20, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 64, 64, 64, 64, 64, 20, 20] 64
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 253
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078340 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078340
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078340/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078340
Building REAL300000078341
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078341'
/scratch/stefan/7769659/working/building/REAL300000078341 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078341

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078341/0 /scratch/stefan/7769659/working/building/REAL300000078341 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/264
`/scratch/stefan/7769659/working/3D/264' -> `0.mol2'
Preparing input files

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

`REAL300000078341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078341 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 6, 6, 12, 12, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 33
rigid atoms, others: [1, 38, 39, 11, 12, 13, 14, 15, 48, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 47
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078341 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 12, 12, 8, 8, 17, 17, 17, 33, 33, 33, 33, 33, 33, 12, 12, 8, 8, 8, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 33, 33, 12, 12] 33
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 134
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078341 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078341
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078341/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078341
Building REAL300000078342
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078342'
/scratch/stefan/7769659/working/building/REAL300000078342 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078342

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078342/0 /scratch/stefan/7769659/working/building/REAL300000078342 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/265
`/scratch/stefan/7769659/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1)

`REAL300000078342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078342 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 1, 1] 4
rigid atoms, others: [1, 45, 38, 39, 44, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 19
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078342 none CC(=NNC(=O)C1CCOC1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 3, 3] 4
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 11
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078342 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078342
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078342/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078342
Building REAL300000078343
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078343'
/scratch/stefan/7769659/working/building/REAL300000078343 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078343

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078343/0 /scratch/stefan/7769659/working/building/REAL300000078343 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/266
`/scratch/stefan/7769659/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1CCOC1)CCC2)

`REAL300000078343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078343 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1CCOC1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 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
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, 10, 10, 1, 10, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32] 32
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38])
total number of confs: 49
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078343 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1CCOC1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 9, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1] 32
rigid atoms, others: [0, 1, 2, 3, 36, 33, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 38, 37, 35] set([32, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 89
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078343 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078343
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078343/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078343
Building REAL300000078344
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078344'
/scratch/stefan/7769659/working/building/REAL300000078344 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078344

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078344/0 /scratch/stefan/7769659/working/building/REAL300000078344 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/267
`/scratch/stefan/7769659/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC(=O)C2CCOC2)C=C1)

`REAL300000078344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078344 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 198, 162, 103, 44, 41, 57, 57, 26, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 57, 57, 201, 201, 162, 162, 57, 57, 26, 9, 1, 1, 1, 1, 1, 1, 1, 57, 57] 201
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 711
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078344 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 26, 30, 14, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 20, 20, 57, 57, 57, 57, 1, 1, 25, 25, 14, 14, 1, 1, 6, 19, 57, 57, 57, 57, 57, 57, 57, 1, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 38, 20, 21, 26, 27, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 283
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078344 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078344
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078344/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078344
Building REAL300000078345
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078345'
/scratch/stefan/7769659/working/building/REAL300000078345 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078345

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078345/0 /scratch/stefan/7769659/working/building/REAL300000078345 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/268
`/scratch/stefan/7769659/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)C1CCOC1)

`REAL300000078345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078345 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [191, 191, 191, 131, 55, 55, 55, 30, 55, 55, 55, 30, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 191, 191, 55, 55, 55, 30, 11, 1, 1, 1, 1, 1, 1, 1] 191
rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 635
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078345 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [76, 47, 76, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 55, 55, 55, 55, 47, 47, 1, 1, 1, 5, 13, 55, 55, 55, 55, 55, 55, 55] 191
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 385
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078345 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078345
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078345/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078345
Building REAL300000078346
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078346'
/scratch/stefan/7769659/working/building/REAL300000078346 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078346

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078346/0 /scratch/stefan/7769659/working/building/REAL300000078346 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/269
`/scratch/stefan/7769659/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)C2CCOC2)=C1)C(=O)[O-])

`REAL300000078346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078346 none CC(OC1=CC=CC(C=NNC(=O)C2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 143, 50, 50, 50, 50, 50, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 21, 9, 1, 1, 1, 1, 1, 1, 1, 50] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 511
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078346 none CC(OC1=CC=CC(C=NNC(=O)C2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 18, 17, 50, 50, 50, 50, 1, 34, 52, 52, 34, 34, 34, 34, 1, 1, 1, 8, 17, 50, 50, 50, 50, 50, 50, 50, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 38, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 310
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078346 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078346
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078346/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078346
Building REAL300000078347
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078347'
/scratch/stefan/7769659/working/building/REAL300000078347 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078347

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078347/0 /scratch/stefan/7769659/working/building/REAL300000078347 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/270
`/scratch/stefan/7769659/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078347 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 178, 129, 51, 51, 51, 51, 51, 22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 51, 201, 201, 178, 178, 51, 51, 51, 22, 10, 1, 1, 1, 1, 1, 1, 1, 51] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 536
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078347 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 38, 49, 23, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 19, 18, 51, 51, 51, 51, 1, 38, 38, 23, 23, 1, 1, 1, 8, 18, 51, 51, 51, 51, 51, 51, 51, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 333
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078347 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078347
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078347/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078347
Building REAL300000078348
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078348'
/scratch/stefan/7769659/working/building/REAL300000078348 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078348

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078348/0 /scratch/stefan/7769659/working/building/REAL300000078348 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/271
`/scratch/stefan/7769659/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078348 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [17, 14, 17, 14, 14, 14, 14, 14, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 18, 17, 35, 35, 35, 35, 1, 14, 14, 14, 14, 6, 6, 1, 1, 1, 8, 17, 35, 35, 35, 35, 35, 35, 35, 1] 84
rigid atoms, others: [33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 138
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078348 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 31, 31, 46, 47, 46, 84, 84, 84, 84, 14, 1, 1, 1, 1, 5, 5, 14, 14, 14, 31, 46, 84, 84, 84, 84, 84, 84, 84, 14] 84
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 245
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078348 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
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, 56, 52, 35, 35, 35, 35, 35, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 35, 84, 84, 84, 84, 56, 56, 35, 35, 35, 15, 8, 1, 1, 1, 1, 1, 1, 1, 35] 84
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 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, 37, 45])
total number of confs: 154
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078348 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078348
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078348/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078348
Building REAL300000078349
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078349'
/scratch/stefan/7769659/working/building/REAL300000078349 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078349

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078349/0 /scratch/stefan/7769659/working/building/REAL300000078349 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/272
`/scratch/stefan/7769659/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1[N+](=O)[O-])

`REAL300000078349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078349 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 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, 192, 196, 107, 18, 18, 72, 72, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 192, 192, 72, 72, 18, 9, 1, 1, 1, 1, 1, 1, 1, 72] 196
rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 710
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078349 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 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: [46, 31, 46, 7, 1, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 72, 72, 72, 72, 1, 1, 1, 2, 2, 31, 31, 1, 1, 11, 41, 72, 72, 72, 72, 72, 72, 72, 1] 196
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 341
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078349 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078349
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078349/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078349
Building REAL300000078350
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078350'
/scratch/stefan/7769659/working/building/REAL300000078350 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078350

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078350/0 /scratch/stefan/7769659/working/building/REAL300000078350 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/273
`/scratch/stefan/7769659/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1)

`REAL300000078350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078350 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [25, 25, 25, 25, 39, 39, 25, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 57, 57, 57, 57, 1, 1, 25, 25, 25, 25, 7, 7, 1, 1, 7, 20, 57, 57, 57, 57, 57, 57, 57, 1, 1, 25] 201
rigid atoms, others: [32, 33, 43, 8, 9, 10, 11, 12, 13, 14, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 253
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078350 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 25, 25, 25, 25, 25, 79, 79, 119, 119, 119, 201, 201, 201, 201, 25, 25, 1, 2, 2, 2, 9, 9, 25, 25, 79, 119, 201, 201, 201, 201, 201, 201, 201, 24, 25, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 580
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078350 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 75, 57, 52, 47, 57, 57, 29, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 75, 75, 57, 57, 29, 8, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201] 201
rigid atoms, others: [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, 35, 43, 44, 45])
total number of confs: 379
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078350 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078350
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078350/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078350
Building REAL300000078351
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078351'
/scratch/stefan/7769659/working/building/REAL300000078351 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078351

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078351/0 /scratch/stefan/7769659/working/building/REAL300000078351 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/274
`/scratch/stefan/7769659/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC(=O)C3CCOC3)=C2)=C1)

`REAL300000078351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078351 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC(=O)C3CCOC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [43, 43, 43, 43, 42, 43, 43, 14, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 17, 17, 17, 17, 1, 43, 42, 43, 43, 14, 14, 1, 1, 1, 7, 13, 17, 17, 17, 17, 17, 17, 17, 1, 43] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45])
total number of confs: 139
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078351 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC(=O)C3CCOC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 43, 43, 43, 43, 43, 116, 116, 168, 168, 168, 201, 201, 201, 201, 43, 1, 1, 1, 1, 9, 9, 43, 43, 43, 116, 168, 201, 201, 201, 201, 201, 201, 201, 43, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 541
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078351 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC(=O)C3CCOC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 49, 33, 17, 17, 17, 17, 17, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 49, 49, 17, 17, 17, 11, 7, 1, 1, 1, 1, 1, 1, 1, 17, 201] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45])
total number of confs: 321
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078351 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078351
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078351/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078351
Building REAL300000078352
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078352'
/scratch/stefan/7769659/working/building/REAL300000078352 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078352

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078352/0 /scratch/stefan/7769659/working/building/REAL300000078352 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/275
`/scratch/stefan/7769659/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)OC=C1)

`REAL300000078352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078352 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 15, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 40, 40, 40, 40, 1, 1, 11, 11, 11, 5, 5, 1, 1, 8, 20, 40, 40, 40, 40, 40, 40, 40, 1, 1, 11, 11] 72
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40, 21, 22, 39, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 151
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078352 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 11, 12, 11, 11, 30, 30, 40, 40, 40, 72, 72, 72, 72, 11, 11, 1, 1, 1, 5, 5, 12, 12, 31, 40, 72, 72, 72, 72, 72, 72, 72, 11, 11, 1, 1] 72
rigid atoms, others: [1, 3, 4, 5, 41, 42, 23, 24, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 220
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078352 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 46, 40, 38, 35, 40, 40, 20, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 40, 40, 72, 72, 72, 46, 46, 40, 40, 20, 8, 1, 1, 1, 1, 1, 1, 1, 40, 40, 72, 72] 72
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 156
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078352 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078352
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078352/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078352
Building REAL300000078353
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078353'
/scratch/stefan/7769659/working/building/REAL300000078353 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078353

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078353/0 /scratch/stefan/7769659/working/building/REAL300000078353 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/276
`/scratch/stefan/7769659/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC(=O)C2CCOC2)C(OCC(=O)[O-])=C1)

`REAL300000078353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078353 none COC1=CC=C(C=NNC(=O)C2CCOC2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 42, 23, 42, 42, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 42, 42, 111, 197, 201, 201, 42, 68, 68, 68, 42, 42, 23, 10, 1, 1, 1, 1, 1, 1, 1, 197, 197, 42] 201
rigid atoms, others: [32, 33, 34, 35, 36, 9, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 719
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078353 none COC1=CC=C(C=NNC(=O)C2CCOC2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 42, 42, 42, 42, 1, 1, 9, 41, 70, 70, 1, 3, 3, 3, 1, 1, 4, 8, 42, 42, 42, 42, 42, 42, 42, 41, 41, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 332
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078353 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078353
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078353/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078353
Building REAL300000078354
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078354'
/scratch/stefan/7769659/working/building/REAL300000078354 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078354

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078354/0 /scratch/stefan/7769659/working/building/REAL300000078354 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/277
`/scratch/stefan/7769659/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1)

`REAL300000078354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078354 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 196, 201, 100, 196, 196, 23, 23, 45, 45, 13, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 45, 45, 45, 45, 13, 8, 1, 1, 1, 1, 1, 1, 1, 45, 45] 201
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 34, 35])
total number of confs: 665
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078354 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 28, 40, 7, 28, 28, 1, 1, 1, 1, 1, 1, 7, 7, 19, 20, 19, 45, 45, 45, 45, 1, 1, 1, 1, 7, 19, 45, 45, 45, 45, 45, 45, 45, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078354 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078354
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078354/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078354
Building REAL300000078355
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078355'
/scratch/stefan/7769659/working/building/REAL300000078355 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078355

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078355/0 /scratch/stefan/7769659/working/building/REAL300000078355 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/278
`/scratch/stefan/7769659/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)C1CCOC1)

`REAL300000078355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078355 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 28, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 51, 51, 51, 51, 28, 9, 1, 1, 1, 1, 1, 1, 1] 51
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078355 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 51, 51, 51, 51, 2, 2, 2, 1, 11, 23, 51, 51, 51, 51, 51, 51, 51] 51
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078355 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078355
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078355/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078355
Building REAL300000078356
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078356'
/scratch/stefan/7769659/working/building/REAL300000078356 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078356

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078356/0 /scratch/stefan/7769659/working/building/REAL300000078356 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/279
`/scratch/stefan/7769659/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Br)

`REAL300000078356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078356 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 146, 35, 32, 57, 57, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 57, 57, 57, 201, 201, 57, 57, 18, 9, 1, 1, 1, 1, 1, 1, 1, 57] 201
rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35])
total number of confs: 564
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078356 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [62, 40, 62, 7, 1, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 57, 57, 57, 57, 1, 1, 1, 40, 40, 1, 1, 8, 29, 57, 57, 57, 57, 57, 57, 57, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 358
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078356 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078356
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078356/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078356
Building REAL300000078357
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078357'
/scratch/stefan/7769659/working/building/REAL300000078357 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078357

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078357/0 /scratch/stefan/7769659/working/building/REAL300000078357 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/280
`/scratch/stefan/7769659/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2CCOC2)C=C1)

`REAL300000078357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078357 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 32, 32, 32, 32, 32, 22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 22, 10, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32
rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 56
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078357 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 13, 13, 13, 32, 32, 32, 32, 1, 1, 3, 3, 3, 1, 6, 13, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32
rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 9, 10, 11, 12, 22, 23, 27, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 92
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078357 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078357
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078357/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078357
Building REAL300000078358
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078358'
/scratch/stefan/7769659/working/building/REAL300000078358 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078358

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078358/0 /scratch/stefan/7769659/working/building/REAL300000078358 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/281
`/scratch/stefan/7769659/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1F)

`REAL300000078358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078358 none CCC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 12, 1, 12, 12, 41, 41, 41, 86, 86, 86, 86, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 32, 32, 32, 32, 32, 41, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1] 91
rigid atoms, others: [2, 35, 36, 37, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 339
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078358 none CCC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [50, 31, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 31, 86, 86, 86, 86, 86, 86, 86, 86, 86, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86] 91
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37])
total number of confs: 234
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078358 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078358
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078358/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078358
Building REAL300000078359
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078359'
/scratch/stefan/7769659/working/building/REAL300000078359 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078359

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078359/0 /scratch/stefan/7769659/working/building/REAL300000078359 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/282
`/scratch/stefan/7769659/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)C3CCOC3)=C2C=C1)

`REAL300000078359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078359 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3CCOC3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 21, 9, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078359 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3CCOC3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 22, 22, 22, 22, 1, 1, 1, 1, 1, 4, 9, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 19, 20, 21, 22, 23, 33] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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
/scratch/stefan/7769659/working/building/REAL300000078359 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078359/1 /scratch/stefan/7769659/working/building/REAL300000078359 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/283
`/scratch/stefan/7769659/working/3D/283' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC(=O)C1CCOC1)

`REAL300000078359.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078359/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078359 none O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 44, 44, 44, 44, 25, 9, 1, 1, 1, 1, 1, 1, 1] 44
rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078359 none O=C([O-])C1=CC=C2C(=C1)NN=C2C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 44, 44, 44, 44, 1, 1, 1, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078359 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078359
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078359/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078359/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078359
Building REAL300000078360
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078360'
/scratch/stefan/7769659/working/building/REAL300000078360 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078360

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078360/0 /scratch/stefan/7769659/working/building/REAL300000078360 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/284
`/scratch/stefan/7769659/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2CCOC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000078360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078360 none COC1=CC(C=NNC(=O)C2CCOC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 36, 36, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 123, 201, 201, 201, 67, 67, 67, 36, 14, 8, 1, 1, 1, 1, 1, 1, 1, 36, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41])
total number of confs: 607
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078360 none COC1=CC(C=NNC(=O)C2CCOC2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 36, 36, 36, 36, 1, 1, 2, 2, 1, 1, 1, 10, 45, 73, 73, 3, 3, 3, 1, 7, 17, 36, 36, 36, 36, 36, 36, 36, 1, 45, 45] 201
rigid atoms, others: [1, 2, 3, 4, 5, 39, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078360 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078360
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078360/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078360
Building REAL300000078361
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078361'
/scratch/stefan/7769659/working/building/REAL300000078361 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078361

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078361/0 /scratch/stefan/7769659/working/building/REAL300000078361 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/285
`/scratch/stefan/7769659/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(=O)C1CCOC1)

`REAL300000078361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078361 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 15, 15, 15, 11, 11, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 15, 15, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1] 15
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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])
total number of confs: 72
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078361 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 2, 2, 2, 5, 5, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11] 15
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 49
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078361 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078361
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078361/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078361
Building REAL300000078362
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078362'
/scratch/stefan/7769659/working/building/REAL300000078362 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078362

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078362/0 /scratch/stefan/7769659/working/building/REAL300000078362 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/286
`/scratch/stefan/7769659/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000078362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078362 none CC(=NNC(=O)C1CCOC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 30, 30, 73, 73, 73, 73, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 30, 73, 73, 73, 73, 73, 73, 73, 1, 1, 19, 19, 19, 19, 1, 1] 199
rigid atoms, others: [1, 45, 38, 39, 44, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 216
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078362 none CC(=NNC(=O)C1CCOC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 31, 73, 73, 31, 31, 170, 196, 197, 198, 198, 199, 199, 198, 197, 73, 73, 31, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 73, 73, 197, 197, 199, 198, 73, 73] 199
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 420
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078362 none CC(=NNC(=O)C1CCOC1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [63, 19, 63, 63, 114, 114, 114, 199, 199, 199, 199, 13, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 63, 63, 63, 114, 199, 199, 199, 199, 199, 199, 199, 19, 19, 1, 1, 1, 1, 19, 19] 199
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: 587
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078362 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078362
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078362/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078362
Building REAL300000078363
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078363'
/scratch/stefan/7769659/working/building/REAL300000078363 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078363

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078363/0 /scratch/stefan/7769659/working/building/REAL300000078363 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/287
`/scratch/stefan/7769659/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCCC(=O)[O-])

`REAL300000078363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078363 none COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 24, 24, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 24, 24, 24, 24, 102, 170, 191, 201, 199, 49, 49, 49, 24, 10, 8, 1, 1, 1, 1, 1, 1, 1, 24, 24, 170, 170, 191, 191] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42])
total number of confs: 662
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078363 none COC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 23, 24, 24, 24, 1, 1, 1, 1, 9, 44, 64, 88, 85, 3, 3, 3, 1, 7, 13, 24, 24, 24, 24, 24, 24, 24, 1, 1, 44, 44, 64, 64] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 401
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078363 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078363
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078363/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078363
Building REAL300000078364
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078364'
/scratch/stefan/7769659/working/building/REAL300000078364 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078364

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078364/0 /scratch/stefan/7769659/working/building/REAL300000078364 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/288
`/scratch/stefan/7769659/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=C(C)N=C1C)

`REAL300000078364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078364 none CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', '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, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 28, 28, 28, 68, 68, 68, 68, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 28, 68, 68, 68, 68, 68, 68, 68, 1, 2, 2, 2, 2, 2, 2] 68
rigid atoms, others: [1, 33, 11, 12, 13, 14, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 197
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078364 none CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', '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, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 34, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 34, 34, 34, 11, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68] 68
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 109
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078364 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078364
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078364/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078364
Building REAL300000078365
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078365'
/scratch/stefan/7769659/working/building/REAL300000078365 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078365

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078365/0 /scratch/stefan/7769659/working/building/REAL300000078365 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/289
`/scratch/stefan/7769659/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1)C(=O)[O-])

`REAL300000078365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078365 none CC(OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 135, 52, 52, 81, 81, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 81, 81, 188, 188, 188, 188, 188, 188, 188, 81, 81, 30, 9, 1, 1, 1, 1, 1, 1, 1, 81, 81] 188
rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 569
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078365 none CC(OC1=CC=C(C=NNC(=O)C2CCOC2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [20, 7, 1, 1, 1, 1, 1, 1, 6, 6, 28, 29, 29, 81, 81, 81, 81, 1, 1, 20, 27, 27, 20, 20, 20, 20, 1, 1, 6, 28, 81, 81, 81, 81, 81, 81, 81, 1, 1] 188
rigid atoms, others: [2, 3, 4, 5, 6, 7, 38, 17, 18, 26, 27, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 299
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078365 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078365
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078365/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078365
Building REAL300000078366
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078366'
/scratch/stefan/7769659/working/building/REAL300000078366 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078366

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078366/0 /scratch/stefan/7769659/working/building/REAL300000078366 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/290
`/scratch/stefan/7769659/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1CCC(=NNC(=O)C2CCOC2)C2=CC=CC=C21)

`REAL300000078366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078366 none O=C([O-])C1CCC(=NNC(=O)C2CCOC2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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, 8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 13
rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38])
total number of confs: 25
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078366 none O=C([O-])C1CCC(=NNC(=O)C2CCOC2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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, 1, 6, 6, 6, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38] set([0, 32, 2, 34, 33, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31])
total number of confs: 39
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078366 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078366
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078366/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078366
Building REAL300000078367
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078367'
/scratch/stefan/7769659/working/building/REAL300000078367 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078367

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078367/0 /scratch/stefan/7769659/working/building/REAL300000078367 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/291
`/scratch/stefan/7769659/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC(=O)C2CCOC2)C2=CC=CC=C21)

`REAL300000078367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078367 none O=C([O-])CN1C=C(C=NNC(=O)C2CCOC2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 85, 85, 85, 44, 44, 11, 11, 1, 11, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 157, 157, 85, 44, 11, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85] 157
rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38])
total number of confs: 457
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078367 none O=C([O-])CN1C=C(C=NNC(=O)C2CCOC2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 12, 1, 1, 1, 1, 1, 6, 6, 29, 29, 28, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 28, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1] 157
rigid atoms, others: [35, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 38, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 259
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078367 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078367
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078367/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078367
Building REAL300000078368
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078368'
/scratch/stefan/7769659/working/building/REAL300000078368 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078368

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078368/0 /scratch/stefan/7769659/working/building/REAL300000078368 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/292
`/scratch/stefan/7769659/working/3D/292' -> `0.mol2'
Preparing input files

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

`REAL300000078368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078368 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 20, 20, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 6, 24, 42, 69, 86, 86, 1, 12, 12, 12, 20, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 24, 24, 42, 42, 69, 69, 1] 201
rigid atoms, others: [1, 35, 36, 37, 44, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 441
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078368 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 72, 120, 152, 201, 201, 201, 27, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 120, 120, 152, 152, 201, 201, 27] 201
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 759
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078368 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078368
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078368/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078368
Building REAL300000078369
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078369'
/scratch/stefan/7769659/working/building/REAL300000078369 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078369

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078369/0 /scratch/stefan/7769659/working/building/REAL300000078369 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/293
`/scratch/stefan/7769659/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1CCOC1)

`REAL300000078369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078369 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 54, 60, 60, 60, 60, 60, 166, 201, 201, 201, 201, 60, 60, 8, 8, 1, 8, 1, 1, 1, 1, 1, 23, 23, 23, 54, 54, 60, 60, 60, 60, 201, 201, 201, 201, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 551
number of broken/clashed sets: 173
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078369 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 4, 2, 1, 1, 1, 1, 1, 1, 11, 27, 27, 37, 37, 1, 1, 14, 14, 38, 38, 38, 60, 60, 60, 60, 14, 14, 14, 4, 4, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 38, 60, 60, 60, 60, 60, 60, 60] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 290
number of broken/clashed sets: 173
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078369 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078369
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078369/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078369
Building REAL300000078370
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078370'
/scratch/stefan/7769659/working/building/REAL300000078370 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078370

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078370/0 /scratch/stefan/7769659/working/building/REAL300000078370 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/294
`/scratch/stefan/7769659/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1)

`REAL300000078370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078370 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 51, 55, 55, 55, 55, 55, 126, 201, 201, 201, 55, 55, 8, 8, 1, 8, 1, 1, 1, 1, 1, 19, 19, 19, 51, 51, 55, 55, 55, 55, 201, 201, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 668
number of broken/clashed sets: 167
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078370 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 4, 2, 1, 1, 1, 1, 1, 1, 6, 24, 43, 43, 1, 1, 14, 14, 38, 38, 38, 55, 55, 55, 55, 14, 14, 14, 4, 4, 2, 2, 1, 1, 24, 24, 1, 1, 38, 55, 55, 55, 55, 55, 55, 55] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 13, 14, 35, 36, 31] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 294
number of broken/clashed sets: 167
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078370 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078370
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078370/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078370
Building REAL300000078371
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078371'
/scratch/stefan/7769659/working/building/REAL300000078371 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078371

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078371/0 /scratch/stefan/7769659/working/building/REAL300000078371 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/295
`/scratch/stefan/7769659/working/3D/295' -> `0.mol2'
Preparing input files

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

`REAL300000078371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078371 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 22, 22, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 12, 12, 12, 22, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 28, 28, 28, 28, 1] 201
rigid atoms, others: [1, 34, 35, 36, 41, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 274
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078371 none CC(=NNC(=O)C1CCOC1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 20, 53, 53, 53, 53, 53, 160, 201, 201, 201, 201, 53, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 201, 201, 201, 201, 53] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 450
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078371 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078371
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078371/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078371
Building REAL300000078372
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078372'
/scratch/stefan/7769659/working/building/REAL300000078372 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078372

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078372/0 /scratch/stefan/7769659/working/building/REAL300000078372 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/296
`/scratch/stefan/7769659/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1)

`REAL300000078372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078372 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 63, 69, 69, 69, 69, 69, 164, 193, 201, 201, 197, 69, 69, 8, 8, 1, 8, 1, 1, 1, 1, 1, 21, 21, 21, 63, 63, 69, 69, 69, 69, 193, 193, 201, 201, 69, 69, 8, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 586
number of broken/clashed sets: 156
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078372 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 4, 2, 1, 1, 1, 1, 1, 1, 6, 19, 24, 35, 32, 1, 1, 14, 14, 47, 47, 47, 69, 69, 69, 69, 14, 14, 14, 4, 4, 2, 2, 1, 1, 19, 19, 24, 24, 1, 1, 47, 69, 69, 69, 69, 69, 69, 69] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 14, 15, 38] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 322
number of broken/clashed sets: 156
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078372 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078372
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078372/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078372
Building REAL300000078373
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078373'
/scratch/stefan/7769659/working/building/REAL300000078373 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078373

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078373/0 /scratch/stefan/7769659/working/building/REAL300000078373 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/297
`/scratch/stefan/7769659/working/3D/297' -> `0.mol2'
Preparing input files

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

`REAL300000078373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078373 none CCC(=NNC(=O)C1CCOC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 6, 6, 8, 8, 8, 26, 26, 26, 26, 1, 1, 1, 1, 1, 6, 9, 21, 25, 35, 42, 45, 1, 1, 9, 9, 9, 9, 9, 8, 26, 26, 26, 26, 26, 26, 26, 1, 1, 9, 9, 21, 21, 25, 25, 35, 35, 1, 1] 201
rigid atoms, others: [2, 39, 40, 12, 13, 14, 15, 16, 49, 50, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 268
number of broken/clashed sets: 196
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078373 none CCC(=NNC(=O)C1CCOC1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 9, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 26, 26, 10, 10, 70, 85, 123, 128, 149, 152, 158, 26, 26, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 26, 26, 85, 85, 123, 123, 128, 128, 149, 149, 26, 26] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 6, 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, 45, 46, 47, 48, 49, 50])
total number of confs: 612
number of broken/clashed sets: 196
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078373 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078373
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078373/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078373
Building REAL300000078374
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078374'
/scratch/stefan/7769659/working/building/REAL300000078374 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078374

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078374/0 /scratch/stefan/7769659/working/building/REAL300000078374 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/298
`/scratch/stefan/7769659/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2CCOC2)C1)

`REAL300000078374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078374 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 26, 4, 4] 26
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078374 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 1, 4, 4, 1, 4, 4, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 1, 1] 26
rigid atoms, others: [1, 3, 4, 37, 38, 10, 11, 12, 13, 21, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078374 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 24, 26, 26, 24, 26, 26, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24] 26
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 52
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078374 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078374
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078374/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078374
Building REAL300000078375
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078375'
/scratch/stefan/7769659/working/building/REAL300000078375 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078375

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078375/0 /scratch/stefan/7769659/working/building/REAL300000078375 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/299
`/scratch/stefan/7769659/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC(=O)C2CCOC2)=CC=C1OCCCC(=O)[O-])

`REAL300000078375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078375 none COC1=CC(C(C)=NNC(=O)C2CCOC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 15, 15, 15, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 15, 15, 15, 15, 58, 125, 159, 201, 201, 201, 25, 25, 25, 15, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 125, 125, 159, 159, 201, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 800
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078375 none COC1=CC(C(C)=NNC(=O)C2CCOC2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 42, 62, 91, 96, 96, 4, 4, 4, 1, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 42, 42, 62, 62, 91, 91] 201
rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 468
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078375 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078375
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078375/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078375
Building REAL300000078376
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078376'
/scratch/stefan/7769659/working/building/REAL300000078376 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078376

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078376/0 /scratch/stefan/7769659/working/building/REAL300000078376 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/300
`/scratch/stefan/7769659/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2CCOC2)C1)

`REAL300000078376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078376 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [14, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 32, 32, 32, 77, 77, 77, 77, 11, 1, 1, 1, 1, 11, 11, 32, 77, 77, 77, 77, 77, 77, 77, 11, 11] 77
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 215
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078376 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 7, 11, 11, 11, 1, 1, 1, 1, 8, 8, 8, 30, 30, 30, 30, 1, 11, 11, 9, 11, 1, 1, 8, 30, 30, 30, 30, 30, 30, 30, 1, 1] 77
rigid atoms, others: [1, 3, 4, 37, 38, 11, 12, 13, 14, 22, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 104
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078376 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [38, 30, 38, 30, 30, 77, 77, 77, 77, 77, 77, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 30, 77, 77, 77, 77, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 30, 30] 77
rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 146
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078376 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078376
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078376/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078376
Building REAL300000078377
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078377'
/scratch/stefan/7769659/working/building/REAL300000078377 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078377

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078377/0 /scratch/stefan/7769659/working/building/REAL300000078377 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/301
`/scratch/stefan/7769659/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)C2CCOC2)C1)

`REAL300000078377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078377 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [15, 11, 15, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 31, 31, 31, 78, 78, 78, 78, 11, 1, 1, 1, 1, 11, 11, 31, 78, 78, 78, 78, 78, 78, 78, 11, 11] 78
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 223
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078377 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 2, 11, 11, 11, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 1, 11, 11, 9, 11, 1, 1, 8, 31, 31, 31, 31, 31, 31, 31, 1, 1] 78
rigid atoms, others: [1, 3, 4, 37, 38, 11, 12, 13, 14, 22, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 114
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078377 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(=NNC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [40, 31, 40, 31, 31, 78, 78, 75, 78, 78, 78, 31, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 31, 78, 78, 78, 78, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 31, 31] 78
rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 167
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078377 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078377
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078377/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078377
Building REAL300000078378
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078378'
/scratch/stefan/7769659/working/building/REAL300000078378 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078378

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078378/0 /scratch/stefan/7769659/working/building/REAL300000078378 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/302
`/scratch/stefan/7769659/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1CCOC1)

`REAL300000078378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078378 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1] 13
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 26
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078378 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 31])
total number of confs: 33
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078378 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078378
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078378/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078378
Building REAL300000078379
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078379'
/scratch/stefan/7769659/working/building/REAL300000078379 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078379

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078379/0 /scratch/stefan/7769659/working/building/REAL300000078379 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/303
`/scratch/stefan/7769659/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078379 none CC(=NNC(=O)C1CCOC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 69, 69, 9, 9, 9, 22, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 42, 42] 201
rigid atoms, others: [1, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 425
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078379 none CC(=NNC(=O)C1CCOC1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 29, 80, 80, 80, 29, 80, 80, 80, 158, 201, 201, 201, 29, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 201, 201] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38])
total number of confs: 644
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078379 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078379
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078379/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078379
Building REAL300000078380
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078380'
/scratch/stefan/7769659/working/building/REAL300000078380 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078380

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078380/0 /scratch/stefan/7769659/working/building/REAL300000078380 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/304
`/scratch/stefan/7769659/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000078380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078380 none CC(=NNC(=O)C1CCOC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 1, 9, 9, 21, 21, 21, 41, 41, 41, 41, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 41, 41, 41, 41, 41, 41, 41, 2, 2, 1, 1, 2, 2, 2, 1] 45
rigid atoms, others: [1, 43, 38, 39, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42])
total number of confs: 139
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078380 none CC(=NNC(=O)C1CCOC1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 25, 41, 41, 45, 45, 45, 41, 41, 41, 41, 41, 41, 41, 41, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 45, 45, 41, 41, 41, 41, 41, 41] 45
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 5, 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, 43])
total number of confs: 93
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078380 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078380
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078380/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078380
Building REAL300000078381
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078381'
/scratch/stefan/7769659/working/building/REAL300000078381 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078381

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078381/0 /scratch/stefan/7769659/working/building/REAL300000078381 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/305
`/scratch/stefan/7769659/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1CCOC1)

`REAL300000078381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078381 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 10, 10, 10, 10, 10, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1] 10
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 21
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078381 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 27
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078381 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078381
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078381/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078381
Building REAL300000078382
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078382'
/scratch/stefan/7769659/working/building/REAL300000078382 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078382

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078382/0 /scratch/stefan/7769659/working/building/REAL300000078382 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/306
`/scratch/stefan/7769659/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC(C=NNC(=O)C2CCOC2)=CC=C1)C1=CC=CC=C1)

`REAL300000078382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078382 none O=C([O-])C(OC1=CC(C=NNC(=O)C2CCOC2)=CC=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 103, 27, 27, 27, 13, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 27, 27, 27, 197, 201, 201, 197, 201, 201, 197, 27, 13, 8, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 201, 201, 197, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 629
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078382 none O=C([O-])C(OC1=CC(C=NNC(=O)C2CCOC2)=CC=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 42, 11, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 27, 27, 27, 27, 1, 1, 1, 34, 48, 48, 34, 48, 48, 34, 1, 4, 10, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 48, 48, 34, 48, 48] 201
rigid atoms, others: [4, 5, 6, 7, 8, 39, 40, 18, 19, 20, 38, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45])
total number of confs: 280
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078382 none O=C([O-])C(OC1=CC(C=NNC(=O)C2CCOC2)=CC=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 1, 4, 11, 48, 48, 48, 98, 98, 121, 121, 121, 201, 201, 201, 201, 48, 48, 48, 1, 1, 1, 1, 1, 1, 4, 48, 98, 121, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 553
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078382 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078382
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078382/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078382
Building REAL300000078383
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078383'
/scratch/stefan/7769659/working/building/REAL300000078383 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078383

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078383/0 /scratch/stefan/7769659/working/building/REAL300000078383 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/307
`/scratch/stefan/7769659/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C)

`REAL300000078383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078383 none CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 32, 32, 32, 106, 106, 106, 106, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 18, 18, 9, 9, 9, 32, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 155
rigid atoms, others: [1, 35, 36, 37, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 324
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078383 none CC(=NNC(=O)C1CCOC1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 12, 12, 1, 12, 1, 1, 1, 1, 1, 31, 106, 106, 106, 106, 106, 106, 106, 106, 106, 155, 155, 155, 31, 31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 155, 155, 155, 155, 155, 155, 155] 155
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 240
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078383 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078383
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078383/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078383
Building REAL300000078384
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078384'
/scratch/stefan/7769659/working/building/REAL300000078384 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078384

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078384/0 /scratch/stefan/7769659/working/building/REAL300000078384 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/308
`/scratch/stefan/7769659/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)C=C1)

`REAL300000078384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078384 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 14, 13, 28, 28, 28, 28, 1, 1, 3, 3, 3, 3, 1, 1, 6, 13, 28, 28, 28, 28, 28, 28, 28, 1, 1, 3, 3] 29
rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 21, 22, 39, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 94
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078384 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
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, 3, 1, 3, 10, 10, 17, 17, 17, 29, 29, 29, 29, 3, 3, 1, 1, 1, 1, 3, 3, 10, 17, 29, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1] 29
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078384 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 26, 29, 26, 29, 29, 26, 23, 26, 26, 23, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 26, 26, 29, 29, 29, 29, 26, 26, 23, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 29, 29] 29
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41])
total number of confs: 85
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078384 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078384
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078384/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078384
Building REAL300000078385
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078385'
/scratch/stefan/7769659/working/building/REAL300000078385 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078385

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078385/0 /scratch/stefan/7769659/working/building/REAL300000078385 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/309
`/scratch/stefan/7769659/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3CCOC3)C2=C1)

`REAL300000078385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078385 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19] 19
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078385 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 4, 4, 8, 8, 8, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 20, 21, 22, 23, 24, 25] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078385 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078385
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078385/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078385
Building REAL300000078386
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078386'
/scratch/stefan/7769659/working/building/REAL300000078386 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078386

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078386/0 /scratch/stefan/7769659/working/building/REAL300000078386 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/310
`/scratch/stefan/7769659/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2CCOC2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000078386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078386 none COC1=CC(C=NNC(=O)C2CCOC2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [130, 80, 80, 79, 35, 35, 8, 8, 1, 8, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 156, 187, 187, 201, 201, 130, 130, 130, 80, 35, 8, 1, 1, 1, 1, 1, 1, 1, 80, 187, 187, 187, 187] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42])
total number of confs: 547
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078386 none COC1=CC(C=NNC(=O)C2CCOC2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 80, 80, 80, 80, 1, 1, 1, 1, 1, 5, 14, 14, 23, 23, 4, 4, 4, 1, 9, 30, 80, 80, 80, 80, 80, 80, 80, 1, 14, 14, 14, 14] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 291
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078386 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078386
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078386/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078386
Building REAL300000078387
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078387'
/scratch/stefan/7769659/working/building/REAL300000078387 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078387

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078387/0 /scratch/stefan/7769659/working/building/REAL300000078387 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/311
`/scratch/stefan/7769659/working/3D/311' -> `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)C2CCOC2)=C1)

`REAL300000078387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078387 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 33, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 79, 33, 9, 1, 1, 1, 1, 1, 1, 1, 79] 79
rigid atoms, others: [11, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 28])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078387 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 79, 79, 79, 79, 1, 8, 28, 79, 79, 79, 79, 79, 79, 79, 1] 79
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078387 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078387
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078387/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078387
Building REAL300000078388
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078388'
/scratch/stefan/7769659/working/building/REAL300000078388 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078388

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078388/0 /scratch/stefan/7769659/working/building/REAL300000078388 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/312
`/scratch/stefan/7769659/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3CCOC3)O2)=CC=C1O)

`REAL300000078388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078388 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3CCOC3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
370  conformations in input
total number of sets (complete confs): 370
using faster count positions algorithm for large data
unique positions, atoms: [23, 13, 23, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 74, 74, 74, 74, 1, 12, 12, 12, 12, 12, 1, 1, 7, 25, 74, 74, 74, 74, 74, 74, 74, 13, 13, 24] 370
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 273
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078388 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3CCOC3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
370  conformations in input
total number of sets (complete confs): 370
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 46, 46, 96, 96, 96, 185, 185, 185, 185, 12, 1, 1, 1, 1, 1, 13, 12, 46, 96, 185, 185, 185, 185, 185, 185, 185, 1, 1, 2] 370
rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 521
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078388 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3CCOC3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
370  conformations in input
total number of sets (complete confs): 370
using faster count positions algorithm for large data
unique positions, atoms: [185, 185, 185, 185, 185, 73, 74, 74, 74, 44, 44, 9, 9, 1, 9, 1, 1, 1, 1, 1, 74, 185, 185, 185, 185, 185, 74, 74, 44, 9, 1, 1, 1, 1, 1, 1, 1, 185, 185, 370] 370
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39])
total number of confs: 628
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078388 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078388
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078388/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078388
Building REAL300000078389
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078389'
/scratch/stefan/7769659/working/building/REAL300000078389 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078389

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078389/0 /scratch/stefan/7769659/working/building/REAL300000078389 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/313
`/scratch/stefan/7769659/working/3D/313' -> `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)C1CCOC1)

`REAL300000078389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078389 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1] 9
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078389 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 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
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, 2, 2, 1, 1, 1, 4, 4, 5, 5, 5, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 9, 9] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078389 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078389
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078389/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078389
Building REAL300000078390
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078390'
/scratch/stefan/7769659/working/building/REAL300000078390 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078390

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078390/0 /scratch/stefan/7769659/working/building/REAL300000078390 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/314
`/scratch/stefan/7769659/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)S2)C=C1)

`REAL300000078390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078390 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 44, 44, 44, 44, 1, 6, 6, 6, 6, 1, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44, 6, 6] 88
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 148
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078390 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 7, 7, 7, 7, 30, 30, 56, 56, 56, 88, 88, 88, 88, 7, 1, 1, 1, 1, 7, 7, 30, 56, 88, 88, 88, 88, 88, 88, 88, 1, 1] 88
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: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078390 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3CCOC3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 44, 88, 44, 88, 88, 44, 44, 44, 44, 26, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 44, 88, 88, 88, 88, 44, 44, 26, 8, 1, 1, 1, 1, 1, 1, 1, 88, 88] 88
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 425
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078390 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078390
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078390/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078390
Building REAL300000078391
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078391'
/scratch/stefan/7769659/working/building/REAL300000078391 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078391

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078391/0 /scratch/stefan/7769659/working/building/REAL300000078391 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/315
`/scratch/stefan/7769659/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)S2)=C1)

`REAL300000078391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078391 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 11, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 85, 85, 85, 85, 1, 12, 11, 12, 12, 1, 1, 9, 28, 85, 85, 85, 85, 85, 85, 85, 12] 191
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 230
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078391 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 58, 58, 113, 113, 113, 191, 191, 191, 191, 12, 1, 1, 1, 1, 12, 12, 58, 113, 191, 191, 191, 191, 191, 191, 191, 1] 191
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 38] set([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: 531
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078391 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [191, 191, 191, 191, 191, 191, 191, 85, 85, 85, 85, 46, 46, 10, 10, 1, 10, 1, 1, 1, 1, 1, 85, 191, 191, 191, 191, 85, 85, 46, 10, 1, 1, 1, 1, 1, 1, 1, 191] 191
rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 283
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078391 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078391
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078391/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078391
Building REAL300000078392
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078392'
/scratch/stefan/7769659/working/building/REAL300000078392 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078392

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078392/0 /scratch/stefan/7769659/working/building/REAL300000078392 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/316
`/scratch/stefan/7769659/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3CCOC3)C2=C1)

`REAL300000078392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078392 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 14, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19] 19
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 34])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078392 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 14, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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
/scratch/stefan/7769659/working/building/REAL300000078392 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078392
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078392/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078392
Building REAL300000078393
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078393'
/scratch/stefan/7769659/working/building/REAL300000078393 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078393

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078393/0 /scratch/stefan/7769659/working/building/REAL300000078393 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/317
`/scratch/stefan/7769659/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3CCOC3)C2=C1)

`REAL300000078393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078393 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37])
total number of confs: 27
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078393 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3CCOC3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37] set([32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078393 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078393
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078393/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078393
Building REAL300000078394
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078394'
/scratch/stefan/7769659/working/building/REAL300000078394 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078394

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078394/0 /scratch/stefan/7769659/working/building/REAL300000078394 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/318
`/scratch/stefan/7769659/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078394 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 37, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 58, 58, 58, 37, 11, 1, 1, 1, 1, 1, 1, 1, 58] 58
rigid atoms, others: [12, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 31])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078394 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 58, 58, 58, 58, 1, 1, 1, 11, 30, 58, 58, 58, 58, 58, 58, 58, 1] 58
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 171
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078394 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078394
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078394/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078394
Building REAL300000078395
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078395'
/scratch/stefan/7769659/working/building/REAL300000078395 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078395

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078395/0 /scratch/stefan/7769659/working/building/REAL300000078395 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/319
`/scratch/stefan/7769659/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078395 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 41, 41, 25, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 41, 41, 82, 25, 7, 1, 1, 1, 1, 1, 1, 1, 41] 82
rigid atoms, others: [13, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 32, 20, 21, 22, 23, 24])
total number of confs: 150
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078395 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 41, 41, 41, 41, 1, 1, 2, 11, 19, 41, 41, 41, 41, 41, 41, 41, 1] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 117
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078395 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078395/1 /scratch/stefan/7769659/working/building/REAL300000078395 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/320
`/scratch/stefan/7769659/working/3D/320' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078395.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078395/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078395 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 15, 15, 11, 6, 1, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [13, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 31])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078395 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 15, 15, 15, 15, 1, 1, 6, 9, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 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
/scratch/stefan/7769659/working/building/REAL300000078395 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078395
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078395/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078395/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078395
Building REAL300000078396
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078396'
/scratch/stefan/7769659/working/building/REAL300000078396 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078396

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078396/0 /scratch/stefan/7769659/working/building/REAL300000078396 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/321
`/scratch/stefan/7769659/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)O1)

`REAL300000078396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078396 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 28, 29, 28, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 87, 87, 87, 87, 1, 1, 28, 28, 28, 7, 7, 1, 1, 10, 35, 87, 87, 87, 87, 87, 87, 87, 1, 1] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 41, 23, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 276
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078396 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 28, 28, 28, 28, 28, 82, 82, 123, 123, 123, 201, 201, 201, 201, 28, 28, 1, 1, 1, 8, 8, 28, 28, 82, 123, 201, 201, 201, 201, 201, 201, 201, 28, 28] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 570
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078396 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3CCOC3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 129, 87, 38, 38, 87, 87, 38, 38, 9, 9, 1, 9, 1, 1, 1, 1, 1, 87, 87, 201, 201, 201, 129, 129, 87, 87, 38, 9, 1, 1, 1, 1, 1, 1, 1, 87, 87] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42])
total number of confs: 588
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078396 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078396
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078396/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078396
Building REAL300000078397
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078397'
/scratch/stefan/7769659/working/building/REAL300000078397 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078397

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078397/0 /scratch/stefan/7769659/working/building/REAL300000078397 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/322
`/scratch/stefan/7769659/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(I)=CC(C=NNC(=O)C2CCOC2)=C1)

`REAL300000078397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078397 none O=C([O-])C1=CC(I)=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 22, 22, 20, 9, 1, 1, 1, 1, 1, 1, 1, 22] 22
rigid atoms, others: [12, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 31])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078397 none O=C([O-])C1=CC(I)=CC(C=NNC(=O)C2CCOC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 22, 22, 22, 22, 1, 1, 1, 5, 8, 22, 22, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078397 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078397
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078397/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078397
Building REAL300000078398
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078398'
/scratch/stefan/7769659/working/building/REAL300000078398 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078398

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078398/0 /scratch/stefan/7769659/working/building/REAL300000078398 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/323
`/scratch/stefan/7769659/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2CCOC2)=C1O)

`REAL300000078398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078398 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2CCOC2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 25, 9, 1, 1, 1, 1, 1, 1, 1, 90] 90
rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078398 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2CCOC2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 9, 21, 45, 45, 45, 45, 45, 45, 45, 2] 90
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 38, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078398 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078398
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078398/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078398
Building REAL300000078399
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078399'
/scratch/stefan/7769659/working/building/REAL300000078399 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078399

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078399/0 /scratch/stefan/7769659/working/building/REAL300000078399 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/324
`/scratch/stefan/7769659/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1)

`REAL300000078399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078399 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 56, 56, 56, 56, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 6, 23, 56, 56, 56, 56, 56, 56, 56, 1, 1, 3] 139
rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 23, 24, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 180
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078399 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 34, 34, 34, 81, 81, 81, 81, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 34, 81, 81, 81, 81, 81, 81, 81, 3, 3, 1] 139
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 44, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 246
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078399 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 139, 81, 81, 81, 81, 81, 56, 56, 56, 56, 32, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 54, 56, 81, 139, 139, 81, 81, 81, 56, 56, 32, 10, 1, 1, 1, 1, 1, 1, 1, 56, 56, 81] 139
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44])
total number of confs: 504
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078399 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078399
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078399/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078399
Building REAL300000078400
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078400'
/scratch/stefan/7769659/working/building/REAL300000078400 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078400

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078400/0 /scratch/stefan/7769659/working/building/REAL300000078400 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/325
`/scratch/stefan/7769659/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Cl)=C1)

`REAL300000078400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078400 none O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 15, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 22, 22, 22, 15, 9, 1, 1, 1, 1, 1, 1, 1, 22] 22
rigid atoms, others: [8, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 28])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078400 none O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 11, 11, 11, 22, 22, 22, 22, 1, 1, 1, 1, 5, 11, 22, 22, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078400 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078400
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078400/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078400
Building REAL300000078401
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078401'
/scratch/stefan/7769659/working/building/REAL300000078401 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078401

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078401/0 /scratch/stefan/7769659/working/building/REAL300000078401 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/326
`/scratch/stefan/7769659/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-])

`REAL300000078401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078401 none CCOC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 54, 16, 16, 16, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 16, 16, 16, 16, 74, 165, 181, 181, 94, 94, 94, 94, 94, 16, 10, 8, 1, 1, 1, 1, 1, 1, 1, 16, 16, 165, 165] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42])
total number of confs: 811
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078401 none CCOC1=CC(C=NNC(=O)C2CCOC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 9, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 15, 16, 16, 16, 1, 1, 1, 1, 9, 39, 72, 72, 32, 32, 32, 32, 32, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 1, 1, 39, 39] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 373
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078401 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078401
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078401/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078401
Building REAL300000078402
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078402'
/scratch/stefan/7769659/working/building/REAL300000078402 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078402

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078402/0 /scratch/stefan/7769659/working/building/REAL300000078402 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/327
`/scratch/stefan/7769659/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1CCOC1)

`REAL300000078402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078402 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [19, 12, 19, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 38, 38, 38, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 27, 38, 68, 68, 68, 68, 68, 68, 68] 68
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078402 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 4, 4, 10, 10, 10, 17, 17, 17, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 4, 10, 17, 17, 17, 17, 17, 17, 17] 68
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078402 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [21, 17, 21, 17, 17, 17, 17, 68, 68, 68, 68, 68, 17, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68, 17, 14, 8, 1, 1, 1, 1, 1, 1, 1] 68
rigid atoms, others: [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, 35])
total number of confs: 169
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078402 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078402
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078402/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078402
Building REAL300000078403
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078403'
/scratch/stefan/7769659/working/building/REAL300000078403 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078403

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078403/0 /scratch/stefan/7769659/working/building/REAL300000078403 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/328
`/scratch/stefan/7769659/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-])

`REAL300000078403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078403 none COC1=CC=C(C)C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 50, 50, 50, 50, 50, 50, 37, 37, 10, 10, 1, 10, 1, 1, 1, 1, 1, 50, 50, 74, 74, 74, 74, 74, 50, 50, 50, 50, 50, 37, 10, 1, 1, 1, 1, 1, 1, 1] 74
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 226
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078403 none COC1=CC=C(C)C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 50, 50, 50, 50, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 5, 18, 50, 50, 50, 50, 50, 50, 50] 74
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 141
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078403 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078403
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078403/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078403
Building REAL300000078404
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078404'
/scratch/stefan/7769659/working/building/REAL300000078404 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078404

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078404/0 /scratch/stefan/7769659/working/building/REAL300000078404 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/329
`/scratch/stefan/7769659/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-])

`REAL300000078404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078404 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 13, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 9, 1, 1, 1, 1, 1, 1, 1] 20
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 36
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078404 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2CCOC2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 6, 6, 10, 10, 10, 20, 20, 20, 20, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 10, 20, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078404 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078404
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078404/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078404
Building REAL300000078405
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078405'
/scratch/stefan/7769659/working/building/REAL300000078405 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078405

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078405/0 /scratch/stefan/7769659/working/building/REAL300000078405 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/330
`/scratch/stefan/7769659/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1)

`REAL300000078405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078405 none CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1] 42
rigid atoms, others: [1, 34, 35, 36, 37, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 111
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078405 none CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 28, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 42
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37])
total number of confs: 72
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078405 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078405
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078405/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078405
Building REAL300000078406
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078406'
/scratch/stefan/7769659/working/building/REAL300000078406 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078406

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078406/0 /scratch/stefan/7769659/working/building/REAL300000078406 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/331
`/scratch/stefan/7769659/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Br)=C1)

`REAL300000078406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078406 none O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 15, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 22, 22, 22, 22, 15, 9, 1, 1, 1, 1, 1, 1, 1, 22] 22
rigid atoms, others: [8, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 28])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078406 none O=C([O-])C1=C(C=NNC(=O)C2CCOC2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 11, 11, 11, 22, 22, 22, 22, 1, 1, 1, 1, 5, 11, 22, 22, 22, 22, 22, 22, 22, 1] 22
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078406 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078406
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078406/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078406
Building REAL300000078407
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078407'
/scratch/stefan/7769659/working/building/REAL300000078407 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078407

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078407/0 /scratch/stefan/7769659/working/building/REAL300000078407 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/332
`/scratch/stefan/7769659/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC(=O)C3CCOC3)C2=CC=C1)

`REAL300000078407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078407 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3CCOC3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 21, 6, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43] 43
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35])
total number of confs: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078407 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3CCOC3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 9, 22, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1] 43
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 33, 35] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078407 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078407
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078407/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078407
Building REAL300000078408
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078408'
/scratch/stefan/7769659/working/building/REAL300000078408 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078408

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078408/0 /scratch/stefan/7769659/working/building/REAL300000078408 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/333
`/scratch/stefan/7769659/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000078408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078408 none CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 21, 21, 21, 21, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 21
rigid atoms, others: [1, 35, 36, 37, 38, 39, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 59
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078408 none CC(=NNC(=O)C1CCOC1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21] 21
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39])
total number of confs: 41
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078408 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078408
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078408/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078408
Building REAL300000078409
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078409'
/scratch/stefan/7769659/working/building/REAL300000078409 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078409

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078409/0 /scratch/stefan/7769659/working/building/REAL300000078409 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/334
`/scratch/stefan/7769659/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)C3CCOC3)=CC=C2O1)

`REAL300000078409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078409 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3CCOC3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 24, 9, 1, 1, 1, 1, 1, 1, 1, 37, 37] 37
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34])
total number of confs: 67
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078409 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3CCOC3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 1, 6, 6, 15, 15, 15, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 6, 15, 37, 37, 37, 37, 37, 37, 37, 1, 1] 37
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 33] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 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
/scratch/stefan/7769659/working/building/REAL300000078409 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078409
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078409/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078409
Building REAL300000078410
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078410'
/scratch/stefan/7769659/working/building/REAL300000078410 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078410

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078410/0 /scratch/stefan/7769659/working/building/REAL300000078410 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/335
`/scratch/stefan/7769659/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)C3CCOC3)=CC=CN12)

`REAL300000078410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078410 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3CCOC3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19] 19
rigid atoms, others: [11, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078410 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3CCOC3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 10, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 18, 19, 20, 21, 22, 33] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078410 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078410
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078410/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078410
Building REAL300000078411
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078411'
/scratch/stefan/7769659/working/building/REAL300000078411 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078411

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078411/0 /scratch/stefan/7769659/working/building/REAL300000078411 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/336
`/scratch/stefan/7769659/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2CCOC2)O1)

`REAL300000078411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078411 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2CCOC2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 80, 80, 80, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 19, 19, 80, 80, 80, 29, 29, 1, 1, 1, 1, 4, 6, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078411 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2CCOC2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 42, 80, 80, 80, 80, 80, 80, 102, 102, 106, 106, 106, 201, 201, 201, 201, 1, 1, 1, 8, 8, 80, 80, 80, 80, 102, 106, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078411 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2CCOC2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 117, 63, 19, 19, 19, 10, 19, 19, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 201, 201, 201, 117, 117, 19, 19, 19, 19, 10, 8, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 518
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078411 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078411
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078411/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078411
Building REAL300000078412
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078412'
/scratch/stefan/7769659/working/building/REAL300000078412 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078412

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078412/0 /scratch/stefan/7769659/working/building/REAL300000078412 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/337
`/scratch/stefan/7769659/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1CCOC1)

`REAL300000078412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078412 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 10, 10, 9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 10, 9, 7, 1, 1, 1, 1, 1, 1, 1] 10
rigid atoms, others: [13, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078412 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 1, 1, 1, 5, 5, 7, 7, 7, 10, 10, 10, 10, 1, 1, 1, 5, 7, 10, 10, 10, 10, 10, 10, 10] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078412 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078412
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078412/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078412
Building REAL300000078413
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078413'
/scratch/stefan/7769659/working/building/REAL300000078413 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078413

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078413/0 /scratch/stefan/7769659/working/building/REAL300000078413 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/338
`/scratch/stefan/7769659/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1CCOC1)

`REAL300000078413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078413 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [77, 68, 68, 68, 68, 68, 77, 68, 68, 68, 68, 68, 68, 69, 69, 36, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 77, 77, 77, 68, 77, 77, 77, 68, 68, 36, 11, 1, 1, 1, 1, 1, 1, 1] 79
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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: 138
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078413 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 17, 17, 17, 68, 68, 68, 68, 3, 3, 3, 1, 3, 3, 3, 1, 1, 8, 17, 68, 68, 68, 68, 68, 68, 68] 79
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 188
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078413 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078413
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078413/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078413
Building REAL300000078414
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078414'
/scratch/stefan/7769659/working/building/REAL300000078414 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078414

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078414/0 /scratch/stefan/7769659/working/building/REAL300000078414 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/339
`/scratch/stefan/7769659/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC(=O)C1CCOC1)

`REAL300000078414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078414 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 27, 27, 27, 27, 11, 7, 1, 1, 1, 1, 1, 1, 1] 27
rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078414 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC(=O)C1CCOC1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 6, 6, 12, 12, 12, 27, 27, 27, 27, 1, 1, 1, 1, 6, 12, 27, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078414 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078414
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078414/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078414
Building REAL300000078415
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078415'
/scratch/stefan/7769659/working/building/REAL300000078415 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078415

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078415/0 /scratch/stefan/7769659/working/building/REAL300000078415 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/340
`/scratch/stefan/7769659/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Cl)

`REAL300000078415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078415 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 145, 59, 31, 59, 59, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 59, 59, 59, 201, 201, 59, 59, 17, 8, 1, 1, 1, 1, 1, 1, 1, 59] 201
rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35])
total number of confs: 595
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078415 none O=C([O-])COC1=CC=C(C=NNC(=O)C2CCOC2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 41, 60, 8, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 59, 59, 59, 59, 1, 1, 1, 41, 41, 1, 1, 9, 34, 59, 59, 59, 59, 59, 59, 59, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 347
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078415 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078415
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078415/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078415
Building REAL300000078416
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078416'
/scratch/stefan/7769659/working/building/REAL300000078416 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078416

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078416/0 /scratch/stefan/7769659/working/building/REAL300000078416 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/341
`/scratch/stefan/7769659/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)C2CCOC2)C=C1)

`REAL300000078416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078416 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 37, 22, 14, 22, 22, 14, 22, 22, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 22, 22, 39, 39, 37, 22, 22, 10, 8, 1, 1, 1, 1, 1, 1, 1, 22, 22] 39
rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078416 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)C2CCOC2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 9, 10, 10, 22, 22, 22, 22, 1, 1, 9, 9, 5, 1, 1, 6, 9, 22, 22, 22, 22, 22, 22, 22, 1, 1] 39
rigid atoms, others: [5, 38, 39, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078416 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078416
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078416/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078416
Building REAL300000078417
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078417'
/scratch/stefan/7769659/working/building/REAL300000078417 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078417

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078417/0 /scratch/stefan/7769659/working/building/REAL300000078417 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/342
`/scratch/stefan/7769659/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC(=O)C3CCOC3)C(F)=CC=C2S1)

`REAL300000078417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078417 none O=C([O-])C1=CC2=C(C=NNC(=O)C3CCOC3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 21, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34])
total number of confs: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078417 none O=C([O-])C1=CC2=C(C=NNC(=O)C3CCOC3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 9, 9, 18, 18, 18, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 9, 18, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 33] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 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
/scratch/stefan/7769659/working/building/REAL300000078417 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078417
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078417/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078417
Building REAL300000078418
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078418'
/scratch/stefan/7769659/working/building/REAL300000078418 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078418

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078418/0 /scratch/stefan/7769659/working/building/REAL300000078418 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/343
`/scratch/stefan/7769659/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3CCOC3)=N2)C1)

`REAL300000078418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078418 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3CCOC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 43, 43, 43, 43, 1, 13, 13, 13, 1, 1, 5, 14, 43, 43, 43, 43, 43, 43, 43, 13, 13] 109
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 181
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078418 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3CCOC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 29, 29, 69, 69, 69, 109, 109, 109, 109, 13, 1, 1, 1, 13, 13, 29, 69, 109, 109, 109, 109, 109, 109, 109, 1, 1] 109
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 38, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 302
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078418 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC(=O)C3CCOC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 109, 109, 109, 43, 109, 43, 43, 43, 33, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 43, 109, 109, 109, 43, 43, 33, 10, 1, 1, 1, 1, 1, 1, 1, 109, 109] 109
rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 235
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078418 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078418
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078418/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078418
Building REAL300000078419
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078419'
/scratch/stefan/7769659/working/building/REAL300000078419 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078419

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078419/0 /scratch/stefan/7769659/working/building/REAL300000078419 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/344
`/scratch/stefan/7769659/working/3D/344' -> `0.mol2'
Preparing input files

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

`REAL300000078419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078419 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(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', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 6, 1, 1, 2, 2, 1, 14, 14] 56
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 28, 29, 31])
total number of confs: 29
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078419 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(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', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 4, 4, 8, 9, 8, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 4, 8, 14, 14, 28, 28, 14, 1, 1] 56
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: 92
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078419 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078419
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078419/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078419
Building REAL300000078420
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078420'
/scratch/stefan/7769659/working/building/REAL300000078420 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078420

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078420/0 /scratch/stefan/7769659/working/building/REAL300000078420 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/345
`/scratch/stefan/7769659/working/3D/345' -> `0.mol2'
Preparing input files

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

`REAL300000078420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078420 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 46, 27, 27, 27, 13, 27, 27, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 27, 27, 27, 27, 13, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [32, 33, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 235
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078420 none O=C([O-])COC1=CC=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [28, 24, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 24, 24, 1, 1, 1, 1, 4, 9, 27, 27, 54, 54, 27] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 240
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078420 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078420
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078420/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078420
Building REAL300000078421
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078421'
/scratch/stefan/7769659/working/building/REAL300000078421 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078421

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078421/0 /scratch/stefan/7769659/working/building/REAL300000078421 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/346
`/scratch/stefan/7769659/working/3D/346' -> `0.mol2'
Preparing input files

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

`REAL300000078421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078421 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 6, 6, 6, 20, 44, 44, 88, 88, 44, 1, 1, 10, 10, 1, 1] 268
rigid atoms, others: [1, 37, 38, 41, 42, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 271
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078421 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 25, 32, 67, 67, 67, 67, 67, 67, 67, 44, 44, 21, 21, 21, 7, 1, 1, 2, 2, 1, 44, 44, 67, 67, 44, 44] 268
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 171
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078421 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [22, 1, 21, 22, 40, 40, 45, 67, 67, 67, 67, 67, 67, 67, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 40, 67, 67, 134, 134, 67, 10, 10, 1, 1, 10, 10] 268
rigid atoms, others: [39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 440
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078421 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078421
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078421/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078421
Building REAL300000078422
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078422'
/scratch/stefan/7769659/working/building/REAL300000078422 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078422

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078422/0 /scratch/stefan/7769659/working/building/REAL300000078422 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/347
`/scratch/stefan/7769659/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-])

`REAL300000078422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078422 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [18, 10, 10, 10, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 67, 67, 67, 18, 18, 18, 10, 5, 5, 1, 1, 2, 2, 1, 10, 10, 67, 67] 268
rigid atoms, others: [32, 33, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40])
total number of confs: 202
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078422 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 9, 19, 19, 19, 3, 3, 3, 1, 4, 4, 10, 10, 20, 20, 10, 1, 1, 19, 19] 268
rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 111
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078422 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078422
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078422/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078422
Building REAL300000078423
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078423'
/scratch/stefan/7769659/working/building/REAL300000078423 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078423

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078423/0 /scratch/stefan/7769659/working/building/REAL300000078423 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/348
`/scratch/stefan/7769659/working/3D/348' -> `0.mol2'
Preparing input files

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

`REAL300000078423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078423 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 34, 17, 10, 22, 22, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 67, 67, 22, 22, 10, 5, 1, 1, 2, 2, 1, 22, 22] 268
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36])
total number of confs: 268
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078423 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [16, 10, 16, 3, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 1, 1, 10, 10, 1, 1, 6, 10, 22, 22, 44, 44, 22, 1, 1] 268
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 22, 23, 36, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 186
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078423 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078423
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078423/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078423
Building REAL300000078424
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078424'
/scratch/stefan/7769659/working/building/REAL300000078424 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078424

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078424/0 /scratch/stefan/7769659/working/building/REAL300000078424 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/349
`/scratch/stefan/7769659/working/3D/349' -> `0.mol2'
Preparing input files

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

`REAL300000078424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078424 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 5, 14, 18, 18, 1, 3, 3, 3, 4, 10, 10, 20, 20, 10, 1, 1, 1, 14, 14, 1] 268
rigid atoms, others: [1, 34, 35, 36, 39, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 119
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078424 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 34, 67, 67, 67, 10, 6, 6, 6, 5, 1, 1, 2, 2, 1, 10, 10, 10, 67, 67, 10] 268
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 231
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078424 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078424
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078424/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078424
Building REAL300000078425
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078425'
/scratch/stefan/7769659/working/building/REAL300000078425 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078425

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078425/0 /scratch/stefan/7769659/working/building/REAL300000078425 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/350
`/scratch/stefan/7769659/working/3D/350' -> `0.mol2'
Preparing input files

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

`REAL300000078425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078425 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 9, 5, 1, 1, 2, 2, 1] 68
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 37
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078425 none O=C([O-])C1=CC=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 6, 8, 17, 17, 34, 34, 17] 68
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25] set([0, 32, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 109
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078425 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078425
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078425/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078425
Building REAL300000078426
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078426'
/scratch/stefan/7769659/working/building/REAL300000078426 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078426

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078426/0 /scratch/stefan/7769659/working/building/REAL300000078426 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/351
`/scratch/stefan/7769659/working/3D/351' -> `0.mol2'
Preparing input files

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

`REAL300000078426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078426 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [6, 1, 6, 6, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 23, 23, 46, 46, 23, 1, 1, 1, 1] 92
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 135
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078426 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 7, 1, 1, 2, 2, 1, 23, 23, 23, 23] 92
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 47
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078426 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078426
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078426/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078426
Building REAL300000078427
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078427'
/scratch/stefan/7769659/working/building/REAL300000078427 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078427

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078427/0 /scratch/stefan/7769659/working/building/REAL300000078427 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/352
`/scratch/stefan/7769659/working/3D/352' -> `0.mol2'
Preparing input files

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

`REAL300000078427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078427 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [4, 1, 4, 4, 10, 10, 10, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 4, 4, 4, 10, 39, 39, 78, 78, 39, 1, 1, 2, 2, 1, 1] 252
rigid atoms, others: [1, 34, 37, 38, 33, 14, 15, 16, 17, 18, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 241
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078427 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 39, 39, 15, 15, 63, 63, 63, 39, 39, 15, 15, 15, 7, 1, 1, 2, 2, 1, 39, 39, 63, 63, 39, 39] 252
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 295
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078427 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078427
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078427/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078427
Building REAL300000078428
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078428'
/scratch/stefan/7769659/working/building/REAL300000078428 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078428

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078428/0 /scratch/stefan/7769659/working/building/REAL300000078428 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/353
`/scratch/stefan/7769659/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(O)C(O)=C1)CCC2)

`REAL300000078428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078428 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(O)C(O)=C1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 7, 1, 1, 2, 2, 1, 26, 26, 26, 26, 26, 26] 104
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39])
total number of confs: 42
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078428 none CC1=C(C(=O)[O-])OC2=C1C(=NNC(=O)C1=CC=C(O)C(O)=C1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 8, 26, 26, 52, 52, 26, 1, 1, 1, 1, 1, 1] 104
rigid atoms, others: [0, 1, 2, 3, 36, 37, 6, 7, 8, 9, 10, 11, 34, 35, 22, 23, 24, 39, 38] set([32, 33, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 156
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078428 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078428
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078428/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078428
Building REAL300000078429
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078429'
/scratch/stefan/7769659/working/building/REAL300000078429 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078429

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078429/0 /scratch/stefan/7769659/working/building/REAL300000078429 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/354
`/scratch/stefan/7769659/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)

`REAL300000078429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078429 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 63, 55, 30, 18, 32, 32, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 67, 67, 63, 63, 32, 32, 18, 5, 1, 1, 2, 2, 1, 32, 32] 268
rigid atoms, others: [33, 34, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 238
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078429 none O=C([O-])CCOC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [14, 11, 14, 8, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 1, 1, 10, 10, 8, 8, 1, 1, 6, 12, 32, 32, 64, 64, 32, 1, 1] 268
rigid atoms, others: [5, 6, 7, 8, 9, 10, 39, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 239
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078429 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078429
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078429/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078429
Building REAL300000078430
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078430'
/scratch/stefan/7769659/working/building/REAL300000078430 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078430

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078430/0 /scratch/stefan/7769659/working/building/REAL300000078430 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/355
`/scratch/stefan/7769659/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1)C(=O)[O-])

`REAL300000078430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078430 none CC(OC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 52, 19, 19, 19, 19, 19, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 67, 67, 67, 67, 67, 67, 67, 19, 19, 19, 9, 5, 1, 1, 2, 2, 1, 19] 268
rigid atoms, others: [34, 35, 38, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 164
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078430 none CC(OC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [19, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 1, 19, 23, 23, 19, 19, 19, 19, 1, 1, 1, 4, 8, 19, 19, 38, 38, 19, 1] 268
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 21, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 182
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078430 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078430
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078430/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078430
Building REAL300000078431
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078431'
/scratch/stefan/7769659/working/building/REAL300000078431 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078431

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078431/0 /scratch/stefan/7769659/working/building/REAL300000078431 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/356
`/scratch/stefan/7769659/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1)

`REAL300000078431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078431 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 63, 50, 16, 16, 16, 16, 16, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 67, 67, 63, 63, 16, 16, 16, 8, 5, 1, 1, 2, 2, 1, 16] 268
rigid atoms, others: [34, 35, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 171
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078431 none O=C([O-])CCOC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [24, 14, 21, 12, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 1, 14, 14, 12, 12, 1, 1, 1, 4, 6, 16, 16, 32, 32, 16, 1] 268
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 24, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 173
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078431 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078431
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078431/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078431
Building REAL300000078432
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078432'
/scratch/stefan/7769659/working/building/REAL300000078432 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078432

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078432/0 /scratch/stefan/7769659/working/building/REAL300000078432 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/357
`/scratch/stefan/7769659/working/3D/357' -> `0.mol2'
Preparing input files

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

`REAL300000078432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078432 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 57, 30, 12, 30, 30, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 67, 67, 30, 30, 8, 5, 1, 1, 2, 2, 1, 30] 268
rigid atoms, others: [33, 34, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38])
total number of confs: 219
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078432 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 15, 15, 1, 1, 6, 10, 30, 30, 60, 60, 30, 1] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 221
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078432 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078432
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078432/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078432
Building REAL300000078433
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078433'
/scratch/stefan/7769659/working/building/REAL300000078433 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078433

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078433/0 /scratch/stefan/7769659/working/building/REAL300000078433 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/358
`/scratch/stefan/7769659/working/3D/358' -> `0.mol2'
Preparing input files

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

`REAL300000078433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078433 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 37, 17, 17, 17, 17, 17, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 67, 67, 17, 17, 17, 8, 5, 1, 1, 2, 2, 1, 17] 268
rigid atoms, others: [32, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 204
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078433 none O=C([O-])COC1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 24, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 1, 18, 18, 1, 1, 1, 3, 6, 17, 17, 34, 34, 17, 1] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 23, 36, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 178
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078433 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078433
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078433/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078433
Building REAL300000078434
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078434'
/scratch/stefan/7769659/working/building/REAL300000078434 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078434

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078434/0 /scratch/stefan/7769659/working/building/REAL300000078434 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/359
`/scratch/stefan/7769659/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)OC=C1)

`REAL300000078434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078434 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [13, 12, 13, 11, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 35, 35, 35, 35, 35, 35, 35, 1, 1, 11, 11, 11, 5, 5, 1, 1, 9, 22, 35, 35, 70, 70, 35, 1, 1, 11, 11] 268
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42, 43])
total number of confs: 246
number of broken/clashed sets: 118
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078434 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 11, 11, 11, 11, 26, 26, 37, 37, 37, 67, 67, 67, 67, 67, 67, 67, 11, 11, 1, 1, 1, 5, 5, 11, 12, 26, 37, 67, 67, 134, 134, 67, 11, 11, 1, 1] 268
rigid atoms, others: [1, 3, 4, 5, 42, 43, 26, 27, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 425
number of broken/clashed sets: 118
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078434 none O=C([O-])C1=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 43, 35, 29, 29, 35, 35, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 67, 67, 67, 43, 43, 35, 35, 17, 5, 1, 1, 2, 2, 1, 35, 35, 67, 67] 268
rigid atoms, others: [35, 36, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 40, 41, 42, 43])
total number of confs: 154
number of broken/clashed sets: 118
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078434 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078434
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078434/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078434
Building REAL300000078435
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078435'
/scratch/stefan/7769659/working/building/REAL300000078435 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078435

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078435/0 /scratch/stefan/7769659/working/building/REAL300000078435 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/360
`/scratch/stefan/7769659/working/3D/360' -> `0.mol2'
Preparing input files

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

`REAL300000078435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078435 none COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [23, 15, 7, 15, 15, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 31, 67, 67, 67, 15, 23, 23, 23, 15, 15, 7, 5, 1, 1, 2, 2, 1, 67, 67, 15] 268
rigid atoms, others: [33, 34, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40])
total number of confs: 267
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078435 none COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 17, 17, 17, 1, 3, 3, 3, 1, 1, 4, 6, 15, 15, 30, 30, 15, 17, 17, 1] 268
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 19, 20, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 148
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078435 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078435
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078435/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078435
Building REAL300000078436
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078436'
/scratch/stefan/7769659/working/building/REAL300000078436 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078436

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078436/0 /scratch/stefan/7769659/working/building/REAL300000078436 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/361
`/scratch/stefan/7769659/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)

`REAL300000078436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078436 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 34, 67, 67, 9, 9, 12, 12, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 5, 5, 1, 1, 2, 2, 1, 12, 12] 268
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36])
total number of confs: 221
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078436 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [22, 17, 22, 5, 17, 17, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 4, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 4, 4, 12, 12, 24, 24, 12, 1, 1] 268
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 140
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078436 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078436
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078436/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078436
Building REAL300000078437
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078437'
/scratch/stefan/7769659/working/building/REAL300000078437 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078437

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078437/0 /scratch/stefan/7769659/working/building/REAL300000078437 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/362
`/scratch/stefan/7769659/working/3D/362' -> `0.mol2'
Preparing input files

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

`REAL300000078437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078437 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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, 43, 43, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 18, 5, 1, 1, 2, 2, 1] 172
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 67
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078437 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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, 2, 2, 1, 1, 1, 1, 1, 11, 11, 24, 24, 24, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 11, 24, 43, 43, 86, 86, 43] 172
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 283
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078437 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078437
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078437/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078437
Building REAL300000078438
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078438'
/scratch/stefan/7769659/working/building/REAL300000078438 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078438

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078438/0 /scratch/stefan/7769659/working/building/REAL300000078438 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/363
`/scratch/stefan/7769659/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)

`REAL300000078438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078438 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 18, 5, 1, 1, 2, 2, 1, 32, 32] 128
rigid atoms, others: [33, 34, 37, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 54
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078438 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 16, 16, 16, 32, 32, 32, 32, 32, 32, 32, 1, 1, 3, 3, 3, 1, 6, 16, 32, 32, 64, 64, 32, 1, 1] 128
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 9, 10, 11, 12, 25, 26, 38, 30] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 204
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078438 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078438
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078438/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078438
Building REAL300000078439
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078439'
/scratch/stefan/7769659/working/building/REAL300000078439 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078439

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078439/0 /scratch/stefan/7769659/working/building/REAL300000078439 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/364
`/scratch/stefan/7769659/working/3D/364' -> `0.mol2'
Preparing input files

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

`REAL300000078439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078439 none CCC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [12, 6, 1, 6, 6, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 36, 36, 72, 72, 36, 1, 1, 1, 1] 184
rigid atoms, others: [2, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 253
number of broken/clashed sets: 79
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078439 none CCC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [27, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 36, 36, 35, 36, 36, 36, 36, 36, 27, 27, 27, 27, 27, 7, 1, 1, 2, 2, 1, 36, 36, 36, 36] 184
rigid atoms, others: [34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38])
total number of confs: 109
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078439 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078439
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078439/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078439
Building REAL300000078440
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078440'
/scratch/stefan/7769659/working/building/REAL300000078440 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078440

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078440/0 /scratch/stefan/7769659/working/building/REAL300000078440 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/365
`/scratch/stefan/7769659/working/3D/365' -> `0.mol2'
Preparing input files

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

`REAL300000078440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078440 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [5, 1, 5, 5, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 9, 25, 25, 50, 50, 25, 1, 1, 1, 1] 100
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 153
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078440 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 5, 1, 1, 2, 2, 1, 25, 25, 25, 25] 100
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 43
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078440 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078440
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078440/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078440
Building REAL300000078441
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078441'
/scratch/stefan/7769659/working/building/REAL300000078441 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078441

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078441/0 /scratch/stefan/7769659/working/building/REAL300000078441 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/366
`/scratch/stefan/7769659/working/3D/366' -> `0.mol2'
Preparing input files

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

`REAL300000078441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078441 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
328  conformations in input
total number of sets (complete confs): 328
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 15, 15, 15, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 40, 41, 82, 82, 41, 1, 1, 1, 2] 328
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 250
number of broken/clashed sets: 88
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078441 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
328  conformations in input
total number of sets (complete confs): 328
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 41, 41, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 7, 1, 1, 2, 2, 1, 41, 41, 41, 82] 328
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36])
total number of confs: 149
number of broken/clashed sets: 88
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078441 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078441
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078441/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078441
Building REAL300000078442
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078442'
/scratch/stefan/7769659/working/building/REAL300000078442 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078442

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078442/0 /scratch/stefan/7769659/working/building/REAL300000078442 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/367
`/scratch/stefan/7769659/working/3D/367' -> `0.mol2'
Preparing input files

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

`REAL300000078442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078442 none CCC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [19, 12, 1, 12, 12, 27, 27, 27, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 19, 19, 19, 19, 19, 27, 64, 64, 128, 128, 64, 1, 1, 1] 268
rigid atoms, others: [2, 36, 37, 38, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 420
number of broken/clashed sets: 196
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078442 none CCC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [40, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 64, 64, 64, 64, 64, 64, 64, 64, 64, 40, 40, 40, 40, 40, 6, 1, 1, 2, 2, 1, 64, 64, 64] 268
rigid atoms, others: [32, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38])
total number of confs: 189
number of broken/clashed sets: 196
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078442 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078442
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078442/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078442
Building REAL300000078443
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078443'
/scratch/stefan/7769659/working/building/REAL300000078443 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078443

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078443/0 /scratch/stefan/7769659/working/building/REAL300000078443 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/368
`/scratch/stefan/7769659/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=C2C=C1)

`REAL300000078443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078443 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 15, 7, 1, 1, 2, 2, 1, 20, 20] 80
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35])
total number of confs: 40
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078443 none O=C([O-])C1=CC2=NNC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 4, 7, 20, 20, 40, 40, 20, 1, 1] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 22, 23, 24, 25, 26] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 117
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078443 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078443/1 /scratch/stefan/7769659/working/building/REAL300000078443 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/369
`/scratch/stefan/7769659/working/3D/369' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=NNC2=C1)

`REAL300000078443.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078443/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078443 none O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [40, 40, 40, 40, 40, 40, 40, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 16, 7, 1, 1, 2, 2, 1, 40, 40] 160
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35])
total number of confs: 70
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078443 none O=C([O-])C1=CC=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 8, 14, 39, 40, 80, 80, 40, 1, 1] 160
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 236
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078443 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078443
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078443/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078443/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078443
Building REAL300000078444
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078444'
/scratch/stefan/7769659/working/building/REAL300000078444 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078444

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078444/0 /scratch/stefan/7769659/working/building/REAL300000078444 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/370
`/scratch/stefan/7769659/working/3D/370' -> `0.mol2'
Preparing input files

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

`REAL300000078444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078444 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [11, 1, 11, 11, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 15, 35, 35, 70, 70, 35, 1, 1, 1, 1] 140
rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 215
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078444 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 35, 35, 35, 35, 15, 15, 15, 7, 1, 1, 2, 2, 1, 35, 35, 35, 35] 140
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 61
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078444 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078444
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078444/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078444
Building REAL300000078445
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078445'
/scratch/stefan/7769659/working/building/REAL300000078445 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078445

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078445/0 /scratch/stefan/7769659/working/building/REAL300000078445 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/371
`/scratch/stefan/7769659/working/3D/371' -> `0.mol2'
Preparing input files

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

`REAL300000078445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078445 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 37, 37, 37, 24, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 67, 67, 37, 24, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 210
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078445 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 1, 1, 8, 8, 1, 4, 13, 37, 37, 74, 74, 37] 268
rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 268
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078445 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078445
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078445/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078445
Building REAL300000078446
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078446'
/scratch/stefan/7769659/working/building/REAL300000078446 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078446

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078446/0 /scratch/stefan/7769659/working/building/REAL300000078446 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/372
`/scratch/stefan/7769659/working/3D/372' -> `0.mol2'
Preparing input files

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

`REAL300000078446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078446 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 21, 63, 67, 134, 134, 67, 1, 1, 1] 268
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 393
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078446 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 67, 67, 67, 67, 67, 67, 67, 67, 67, 17, 17, 17, 7, 1, 1, 2, 2, 1, 67, 67, 67] 268
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35])
total number of confs: 99
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078446 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078446
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078446/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078446
Building REAL300000078447
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078447'
/scratch/stefan/7769659/working/building/REAL300000078447 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078447

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078447/0 /scratch/stefan/7769659/working/building/REAL300000078447 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/373
`/scratch/stefan/7769659/working/3D/373' -> `0.mol2'
Preparing input files

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

`REAL300000078447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078447 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [33, 33, 33, 33, 33, 33, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 19, 7, 1, 1, 2, 2, 1, 33] 132
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 26, 27, 29])
total number of confs: 59
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078447 none O=C([O-])C1=CSC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 1, 1, 8, 14, 33, 33, 66, 66, 33, 1] 132
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 194
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078447 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078447
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078447/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078447
Building REAL300000078448
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078448'
/scratch/stefan/7769659/working/building/REAL300000078448 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078448

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078448/0 /scratch/stefan/7769659/working/building/REAL300000078448 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/374
`/scratch/stefan/7769659/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCCC(=O)[O-])

`REAL300000078448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078448 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 11, 11, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 54, 54, 67, 57, 21, 21, 21, 11, 5, 5, 1, 1, 2, 2, 1, 11, 11, 54, 54, 54, 54] 268
rigid atoms, others: [33, 34, 37, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 214
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078448 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 19, 17, 3, 3, 3, 1, 5, 5, 11, 11, 22, 22, 11, 1, 1, 11, 11, 11, 11] 268
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 18, 19, 20, 21, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 119
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078448 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078448
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078448/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078448
Building REAL300000078449
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078449'
/scratch/stefan/7769659/working/building/REAL300000078449 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078449

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078449/0 /scratch/stefan/7769659/working/building/REAL300000078449 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/375
`/scratch/stefan/7769659/working/3D/375' -> `0.mol2'
Preparing input files

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

`REAL300000078449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078449 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [24, 24, 24, 24, 24, 24, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 17, 5, 1, 1, 2, 2, 1, 24] 96
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 45
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078449 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 9, 9, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 9, 15, 24, 24, 48, 48, 24, 1] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 153
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078449 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078449
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078449/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078449
Building REAL300000078450
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078450'
/scratch/stefan/7769659/working/building/REAL300000078450 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078450

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078450/0 /scratch/stefan/7769659/working/building/REAL300000078450 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/376
`/scratch/stefan/7769659/working/3D/376' -> `0.mol2'
Preparing input files

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

`REAL300000078450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078450 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
244  conformations in input
total number of sets (complete confs): 244
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 20, 61, 61, 122, 122, 61, 1, 2, 2, 2, 2, 2, 2] 244
rigid atoms, others: [1, 34, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 377
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078450 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
244  conformations in input
total number of sets (complete confs): 244
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 19, 19, 19, 7, 1, 1, 2, 2, 1, 61, 61, 61, 61, 61, 61, 61] 244
rigid atoms, others: [33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078450 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078450
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078450/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078450
Building REAL300000078451
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078451'
/scratch/stefan/7769659/working/building/REAL300000078451 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078451

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078451/0 /scratch/stefan/7769659/working/building/REAL300000078451 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/377
`/scratch/stefan/7769659/working/3D/377' -> `0.mol2'
Preparing input files

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

`REAL300000078451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078451 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
256  conformations in input
total number of sets (complete confs): 256
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 14, 5, 1, 1, 2, 2, 1, 32, 32, 64] 256
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31, 32, 33])
total number of confs: 116
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078451 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
256  conformations in input
total number of sets (complete confs): 256
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 12, 32, 32, 64, 64, 32, 1, 1, 2] 256
rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 199
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078451 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078451
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078451/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078451
Building REAL300000078452
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078452'
/scratch/stefan/7769659/working/building/REAL300000078452 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078452

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078452/0 /scratch/stefan/7769659/working/building/REAL300000078452 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/378
`/scratch/stefan/7769659/working/3D/378' -> `0.mol2'
Preparing input files

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

`REAL300000078452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078452 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 29, 29, 58, 58, 29, 1, 1, 1, 2, 2, 2] 116
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 175
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078452 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 20, 7, 1, 1, 2, 2, 1, 29, 29, 29, 29, 29, 29] 116
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 54
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078452 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078452
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078452/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078452
Building REAL300000078453
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078453'
/scratch/stefan/7769659/working/building/REAL300000078453 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078453

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078453/0 /scratch/stefan/7769659/working/building/REAL300000078453 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/379
`/scratch/stefan/7769659/working/3D/379' -> `0.mol2'
Preparing input files

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

`REAL300000078453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078453 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [6, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 15, 15, 30, 30, 15, 1, 1] 60
rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 88
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078453 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 7, 1, 1, 2, 2, 1, 15, 15] 60
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 30] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31])
total number of confs: 35
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078453 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078453
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078453/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078453
Building REAL300000078454
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078454'
/scratch/stefan/7769659/working/building/REAL300000078454 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078454

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078454/0 /scratch/stefan/7769659/working/building/REAL300000078454 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/380
`/scratch/stefan/7769659/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)C(=O)[O-])

`REAL300000078454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078454 none CC(OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 47, 16, 10, 30, 30, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 67, 67, 67, 67, 67, 67, 67, 30, 30, 10, 5, 1, 1, 2, 2, 1, 30, 30] 268
rigid atoms, others: [33, 34, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 253
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078454 none CC(OC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 1, 1, 13, 18, 18, 13, 13, 13, 13, 1, 1, 6, 11, 30, 30, 60, 60, 30, 1, 1] 268
rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 20, 21, 38, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 232
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078454 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078454
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078454/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078454
Building REAL300000078455
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078455'
/scratch/stefan/7769659/working/building/REAL300000078455 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078455

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078455/0 /scratch/stefan/7769659/working/building/REAL300000078455 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/381
`/scratch/stefan/7769659/working/3D/381' -> `0.mol2'
Preparing input files

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

`REAL300000078455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078455 none O=C([O-])C1CCC(=NNC(=O)C2=CC=C(O)C(O)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 2, 2, 1, 11, 11, 11, 11] 44
rigid atoms, others: [32, 35, 9, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39])
total number of confs: 25
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078455 none O=C([O-])C1CCC(=NNC(=O)C2=CC=C(O)C(O)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 22, 22, 11, 1, 1, 1, 1] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39] set([0, 32, 2, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 30, 31])
total number of confs: 69
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078455 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078455
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078455/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078455
Building REAL300000078456
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078456'
/scratch/stefan/7769659/working/building/REAL300000078456 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078456

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078456/0 /scratch/stefan/7769659/working/building/REAL300000078456 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/382
`/scratch/stefan/7769659/working/3D/382' -> `0.mol2'
Preparing input files

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

`REAL300000078456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078456 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 37, 37, 37, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 67, 67, 37, 17, 5, 1, 1, 2, 2, 1, 37, 37, 37, 37] 268
rigid atoms, others: [32, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39])
total number of confs: 195
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078456 none O=C([O-])CN1C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 9, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 7, 7, 1, 4, 10, 37, 37, 74, 74, 37, 1, 1, 1, 1] 268
rigid atoms, others: [3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 24, 25, 38, 28, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 239
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078456 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078456
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078456/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078456
Building REAL300000078457
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078457'
/scratch/stefan/7769659/working/building/REAL300000078457 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078457

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078457/0 /scratch/stefan/7769659/working/building/REAL300000078457 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/383
`/scratch/stefan/7769659/working/3D/383' -> `0.mol2'
Preparing input files

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

`REAL300000078457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078457 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 15, 7, 1, 1, 2, 2, 1, 27] 108
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33])
total number of confs: 47
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078457 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 8, 9, 8, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 6, 8, 27, 27, 54, 54, 27, 1] 108
rigid atoms, others: [0, 1, 2, 3, 33, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 166
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078457 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078457
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078457/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078457
Building REAL300000078458
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078458'
/scratch/stefan/7769659/working/building/REAL300000078458 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078458

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078458/0 /scratch/stefan/7769659/working/building/REAL300000078458 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/384
`/scratch/stefan/7769659/working/3D/384' -> `0.mol2'
Preparing input files

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

`REAL300000078458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078458 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [21, 21, 21, 21, 21, 21, 21, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 13, 5, 1, 1, 2, 2, 1, 21] 84
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 32, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 39
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078458 none O=C([O-])C1=CC=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 7, 7, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 7, 9, 21, 21, 42, 42, 21, 1] 84
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078458 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078458
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078458/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078458
Building REAL300000078459
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078459'
/scratch/stefan/7769659/working/building/REAL300000078459 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078459

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078459/0 /scratch/stefan/7769659/working/building/REAL300000078459 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/385
`/scratch/stefan/7769659/working/3D/385' -> `0.mol2'
Preparing input files

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

`REAL300000078459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078459 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 6, 12, 13, 18, 22, 22, 1, 3, 3, 3, 4, 10, 10, 20, 20, 10, 1, 1, 1, 12, 12, 12, 12, 18, 18, 1] 268
rigid atoms, others: [1, 36, 37, 38, 45, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44])
total number of confs: 137
number of broken/clashed sets: 118
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078459 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 28, 65, 65, 67, 67, 67, 10, 6, 6, 6, 5, 1, 1, 2, 2, 1, 10, 10, 10, 65, 65, 65, 65, 67, 67, 10] 268
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 222
number of broken/clashed sets: 118
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078459 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078459
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078459/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078459
Building REAL300000078460
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078460'
/scratch/stefan/7769659/working/building/REAL300000078460 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078460

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078460/0 /scratch/stefan/7769659/working/building/REAL300000078460 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/386
`/scratch/stefan/7769659/working/3D/386' -> `0.mol2'
Preparing input files

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

`REAL300000078460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078460 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 20, 20, 20, 20, 20, 20, 63, 67, 67, 67, 67, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 20, 20, 20, 20, 20, 67, 67, 67, 67, 20, 20, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [44, 45, 48, 18, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 148
number of broken/clashed sets: 238
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078460 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 2, 1, 1, 1, 1, 1, 1, 8, 14, 14, 17, 17, 1, 1, 3, 3, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 2, 2, 1, 1, 14, 14, 14, 14, 1, 1, 8, 20, 20, 40, 40, 20] 268
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 175
number of broken/clashed sets: 238
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078460 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078460
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078460/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078460
Building REAL300000078461
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078461'
/scratch/stefan/7769659/working/building/REAL300000078461 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078461

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078461/0 /scratch/stefan/7769659/working/building/REAL300000078461 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/387
`/scratch/stefan/7769659/working/3D/387' -> `0.mol2'
Preparing input files

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

`REAL300000078461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078461 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 13, 13, 13, 13, 13, 13, 36, 67, 67, 67, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 13, 13, 67, 67, 13, 13, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [41, 42, 45, 17, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 260
number of broken/clashed sets: 268
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078461 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 2, 1, 1, 1, 1, 1, 1, 6, 14, 19, 19, 1, 1, 3, 3, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 2, 2, 1, 1, 14, 14, 1, 1, 5, 13, 13, 26, 26, 13] 268
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43, 44, 45])
total number of confs: 145
number of broken/clashed sets: 268
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078461 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078461
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078461/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078461
Building REAL300000078462
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078462'
/scratch/stefan/7769659/working/building/REAL300000078462 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078462

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078462/0 /scratch/stefan/7769659/working/building/REAL300000078462 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/388
`/scratch/stefan/7769659/working/3D/388' -> `0.mol2'
Preparing input files

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

`REAL300000078462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078462 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 10, 17, 17, 19, 19, 1, 6, 6, 6, 8, 23, 23, 46, 46, 23, 1, 1, 1, 17, 17, 17, 17, 1] 268
rigid atoms, others: [1, 35, 36, 37, 42, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41])
total number of confs: 186
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078462 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 23, 52, 67, 67, 67, 67, 23, 11, 11, 11, 5, 1, 1, 2, 2, 1, 23, 23, 23, 67, 67, 67, 67, 23] 268
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 174
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078462 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078462
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078462/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078462
Building REAL300000078463
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078463'
/scratch/stefan/7769659/working/building/REAL300000078463 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078463

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078463/0 /scratch/stefan/7769659/working/building/REAL300000078463 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/389
`/scratch/stefan/7769659/working/3D/389' -> `0.mol2'
Preparing input files

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

`REAL300000078463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078463 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 18, 18, 18, 18, 18, 18, 61, 67, 67, 67, 61, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 67, 67, 67, 67, 18, 18, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [44, 45, 48, 18, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 170
number of broken/clashed sets: 268
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078463 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 15, 13, 1, 1, 5, 5, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 4, 4, 2, 2, 1, 1, 8, 8, 8, 8, 1, 1, 7, 18, 18, 36, 36, 18] 268
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 159
number of broken/clashed sets: 268
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078463 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078463
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078463/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078463
Building REAL300000078464
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078464'
/scratch/stefan/7769659/working/building/REAL300000078464 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078464

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078464/0 /scratch/stefan/7769659/working/building/REAL300000078464 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/390
`/scratch/stefan/7769659/working/3D/390' -> `0.mol2'
Preparing input files

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

`REAL300000078464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078464 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [9, 1, 9, 9, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 13, 36, 36, 72, 72, 36, 1, 1] 144
rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 217
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078464 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 7, 1, 1, 2, 2, 1, 36, 36] 144
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 30] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31])
total number of confs: 61
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078464 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078464
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078464/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078464
Building REAL300000078465
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078465'
/scratch/stefan/7769659/working/building/REAL300000078465 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078465

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078465/0 /scratch/stefan/7769659/working/building/REAL300000078465 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/391
`/scratch/stefan/7769659/working/3D/391' -> `0.mol2'
Preparing input files

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

`REAL300000078465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078465 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 3, 1, 1, 1, 1, 1, 3, 3, 7, 20, 20, 40, 40, 20, 3, 3] 80
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 120
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078465 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 1, 3, 3, 1, 3, 3, 1, 1, 5, 17, 17, 34, 34, 17, 1, 1] 80
rigid atoms, others: [1, 3, 4, 38, 10, 11, 12, 13, 24, 39, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 109
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078465 none O=C([O-])C1(C2=CC=CC=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 20, 20, 17, 20, 20, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 20, 17, 20, 20, 17, 17, 5, 1, 1, 2, 2, 1, 17, 17] 80
rigid atoms, others: [33, 34, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 46
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078465 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078465
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078465/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078465
Building REAL300000078466
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078466'
/scratch/stefan/7769659/working/building/REAL300000078466 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078466

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078466/0 /scratch/stefan/7769659/working/building/REAL300000078466 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/392
`/scratch/stefan/7769659/working/3D/392' -> `0.mol2'
Preparing input files

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

`REAL300000078466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078466 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [6, 1, 6, 6, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 6, 6, 6, 15, 35, 35, 70, 70, 35, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 196
rigid atoms, others: [1, 35, 36, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 250
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078466 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 19, 19, 19, 6, 1, 1, 2, 2, 1, 35, 35, 49, 49, 35, 35, 35, 35, 35, 35] 196
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 170
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078466 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078466
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078466/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078466
Building REAL300000078467
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078467'
/scratch/stefan/7769659/working/building/REAL300000078467 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078467

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078467/0 /scratch/stefan/7769659/working/building/REAL300000078467 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/393
`/scratch/stefan/7769659/working/3D/393' -> `0.mol2'
Preparing input files

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

`REAL300000078467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078467/0/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']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078467 none CC(CCCCCCC(=O)[O-])=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 34, 33, 45, 40, 56, 67, 67, 67, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 34, 34, 40, 40, 42, 42, 48, 48, 56, 56, 67, 67, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [39, 40, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 370
number of broken/clashed sets: 265
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078467 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078467
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078467/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078467
Building REAL300000078468
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078468'
/scratch/stefan/7769659/working/building/REAL300000078468 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078468

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078468/0 /scratch/stefan/7769659/working/building/REAL300000078468 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/394
`/scratch/stefan/7769659/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1CC(=O)[O-])

`REAL300000078468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078468 none CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 39, 39, 39, 21, 21, 21, 21, 7, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 39, 39] 156
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 124
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078468 none CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 7, 9, 9, 2, 2, 2, 1, 6, 21, 21, 42, 42, 21, 1, 1, 1, 1, 1, 7, 7] 156
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 35, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 152
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078468 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078468
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078468/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078468
Building REAL300000078469
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078469'
/scratch/stefan/7769659/working/building/REAL300000078469 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078469

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078469/0 /scratch/stefan/7769659/working/building/REAL300000078469 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/395
`/scratch/stefan/7769659/working/3D/395' -> `0.mol2'
Preparing input files

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

`REAL300000078469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078469 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [10, 1, 10, 10, 17, 17, 17, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 16, 38, 38, 76, 76, 38, 1, 1] 152
rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 241
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078469 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 38, 38, 38, 38, 38, 38, 38, 19, 19, 19, 7, 1, 1, 2, 2, 1, 38, 38] 152
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 30] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 31])
total number of confs: 62
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078469 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078469
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078469/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078469
Building REAL300000078470
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078470'
/scratch/stefan/7769659/working/building/REAL300000078470 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078470

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078470/0 /scratch/stefan/7769659/working/building/REAL300000078470 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/396
`/scratch/stefan/7769659/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC(C(=O)[O-])C1(C)C)

`REAL300000078470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078470 none CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 44
rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 25
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078470 none CC1C(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 1, 5, 11, 11, 22, 22, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 44
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 34, 15, 16, 17, 18, 35, 21, 22, 23, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44])
total number of confs: 87
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078470 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078470
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078470/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078470
Building REAL300000078471
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078471'
/scratch/stefan/7769659/working/building/REAL300000078471 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078471

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078471/0 /scratch/stefan/7769659/working/building/REAL300000078471 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/397
`/scratch/stefan/7769659/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(O)C(O)=C1)

`REAL300000078471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078471 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 2, 2, 1] 76
rigid atoms, others: [34, 35, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 33
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078471 none CC1CC(C(=O)[O-])CCC1=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 38, 38, 19] 76
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 32, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 37])
total number of confs: 123
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078471 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078471
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078471/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078471
Building REAL300000078472
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078472'
/scratch/stefan/7769659/working/building/REAL300000078472 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078472

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078472/0 /scratch/stefan/7769659/working/building/REAL300000078472 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/398
`/scratch/stefan/7769659/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1C(=O)[O-])

`REAL300000078472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078472 none CC1CC(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 2, 2, 1, 18, 18, 18, 18, 18] 72
rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 32
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078472 none CC1CC(=NNC(=O)C2=CC=C(O)C(O)=C2)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 8, 18, 18, 36, 36, 18, 1, 1, 1, 1, 1] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 38, 34, 16, 17, 18, 35, 25, 26, 27, 37, 36] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 117
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078472 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078472
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078472/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078472
Building REAL300000078473
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078473'
/scratch/stefan/7769659/working/building/REAL300000078473 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078473

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078473/0 /scratch/stefan/7769659/working/building/REAL300000078473 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/399
`/scratch/stefan/7769659/working/3D/399' -> `0.mol2'
Preparing input files

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

`REAL300000078473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078473 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [14, 10, 14, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 25, 59, 59, 59, 59, 59, 59, 59, 10, 1, 1, 1, 1, 10, 10, 25, 59, 59, 118, 118, 59, 10, 10] 236
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 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: 369
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078473 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 10, 10, 5, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 1, 10, 10, 8, 10, 1, 1, 5, 20, 20, 40, 40, 20, 1, 1] 236
rigid atoms, others: [1, 3, 4, 38, 39, 11, 12, 13, 14, 25, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 144
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078473 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(=NNC(=O)C2=CC=C(O)C(O)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [27, 20, 27, 20, 20, 59, 59, 58, 59, 59, 59, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 59, 59, 59, 59, 20, 20, 5, 1, 1, 2, 2, 1, 20, 20] 236
rigid atoms, others: [33, 34, 37, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 124
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078473 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078473
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078473/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078473
Building REAL300000078474
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078474'
/scratch/stefan/7769659/working/building/REAL300000078474 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078474

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078474/0 /scratch/stefan/7769659/working/building/REAL300000078474 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/400
`/scratch/stefan/7769659/working/3D/400' -> `0.mol2'
Preparing input files

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

`REAL300000078474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078474 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 2, 2, 1] 52
rigid atoms, others: [35, 36, 39, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 27
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078474 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 26, 26, 13] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 77
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078474 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078474
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078474/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078474
Building REAL300000078475
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078475'
/scratch/stefan/7769659/working/building/REAL300000078475 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078475

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078475/0 /scratch/stefan/7769659/working/building/REAL300000078475 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/401
`/scratch/stefan/7769659/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(O)C(O)=C1)

`REAL300000078475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078475 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [17, 17, 17, 56, 65, 65, 65, 65, 65, 65, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 56, 56, 65, 65, 65, 65, 65, 65, 5, 1, 1, 2, 2, 1] 260
rigid atoms, others: [34, 35, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 223
number of broken/clashed sets: 206
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078475 none CC(CC1(C(=O)[O-])CCC1)=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 7, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 28, 28, 28, 65, 65, 65, 65, 65, 65, 65, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 28, 65, 65, 130, 130, 65] 260
rigid atoms, others: [32, 2, 3, 4, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38])
total number of confs: 420
number of broken/clashed sets: 206
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078475 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078475
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078475/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078475
Building REAL300000078476
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078476'
/scratch/stefan/7769659/working/building/REAL300000078476 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078476

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078476/0 /scratch/stefan/7769659/working/building/REAL300000078476 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/402
`/scratch/stefan/7769659/working/3D/402' -> `0.mol2'
Preparing input files

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

`REAL300000078476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078476 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
2  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: [9, 1, 9, 9, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 35, 35, 70, 70, 35, 2, 2, 1, 1, 2, 2, 2, 1] 160
rigid atoms, others: [1, 39, 40, 44, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43])
total number of confs: 239
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078476 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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]
2  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: [19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 35, 35, 40, 40, 40, 35, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 5, 1, 1, 2, 2, 1, 40, 40, 35, 35, 35, 35, 35, 35] 160
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 93
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078476 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078476
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078476/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078476
Building REAL300000078477
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078477'
/scratch/stefan/7769659/working/building/REAL300000078477 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078477

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078477/0 /scratch/stefan/7769659/working/building/REAL300000078477 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/403
`/scratch/stefan/7769659/working/3D/403' -> `0.mol2'
Preparing input files

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

`REAL300000078477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078477 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 23, 7, 1, 1, 2, 2, 1] 196
rigid atoms, others: [34, 35, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 75
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078477 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 18, 18, 18, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 1, 2, 2, 2, 1, 10, 18, 49, 49, 98, 98, 49] 196
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 307
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078477 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078477
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078477/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078477
Building REAL300000078478
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078478'
/scratch/stefan/7769659/working/building/REAL300000078478 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078478

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078478/0 /scratch/stefan/7769659/working/building/REAL300000078478 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/404
`/scratch/stefan/7769659/working/3D/404' -> `0.mol2'
Preparing input files

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

`REAL300000078478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078478 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 14, 5, 1, 1, 2, 2, 1, 26, 26, 26] 104
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 27, 28, 30, 31])
total number of confs: 44
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078478 none O=C([O-])C1=C(Cl)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 11, 26, 26, 52, 52, 26, 1, 1, 1] 104
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 163
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078478 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078478
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078478/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078478
Building REAL300000078479
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078479'
/scratch/stefan/7769659/working/building/REAL300000078479 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078479

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078479/0 /scratch/stefan/7769659/working/building/REAL300000078479 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/405
`/scratch/stefan/7769659/working/3D/405' -> `0.mol2'
Preparing input files

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

`REAL300000078479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078479 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 2, 2, 1] 36
rigid atoms, others: [38, 39, 42, 16, 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, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 23
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078479 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 18, 18, 9] 36
rigid atoms, others: [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] set([37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 52
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078479 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078479
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078479/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078479
Building REAL300000078480
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078480'
/scratch/stefan/7769659/working/building/REAL300000078480 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078480

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078480/0 /scratch/stefan/7769659/working/building/REAL300000078480 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/406
`/scratch/stefan/7769659/working/3D/406' -> `0.mol2'
Preparing input files

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

`REAL300000078480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078480 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 11, 5, 1, 1, 2, 2, 1] 68
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 37
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078480 none CN1N=CC(C(=O)[O-])=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 3, 3, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 6, 8, 17, 17, 34, 34, 17] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 25] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 115
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078480 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078480
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078480/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078480
Building REAL300000078481
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078481'
/scratch/stefan/7769659/working/building/REAL300000078481 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078481

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078481/0 /scratch/stefan/7769659/working/building/REAL300000078481 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/407
`/scratch/stefan/7769659/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1F)

`REAL300000078481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078481 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
212  conformations in input
total number of sets (complete confs): 212
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 27, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 27, 7, 1, 1, 2, 2, 1, 53] 212
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 95
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078481 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
212  conformations in input
total number of sets (complete confs): 212
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 7, 15, 53, 53, 106, 106, 53, 1] 212
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 311
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078481 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078481
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078481/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078481
Building REAL300000078482
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078482'
/scratch/stefan/7769659/working/building/REAL300000078482 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078482

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078482/0 /scratch/stefan/7769659/working/building/REAL300000078482 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/408
`/scratch/stefan/7769659/working/3D/408' -> `0.mol2'
Preparing input files

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

`REAL300000078482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078482 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 34, 34, 34, 34, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 34, 67, 67, 34, 34, 23, 6, 1, 1, 2, 2, 1] 268
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 156
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078482 none O=C([O-])C=CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [21, 12, 22, 12, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 34, 34, 34, 34, 34, 34, 34, 1, 12, 12, 1, 1, 4, 13, 34, 34, 68, 68, 34] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 257
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078482 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078482
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078482/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078482
Building REAL300000078483
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078483'
/scratch/stefan/7769659/working/building/REAL300000078483 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078483

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078483/0 /scratch/stefan/7769659/working/building/REAL300000078483 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/409
`/scratch/stefan/7769659/working/3D/409' -> `0.mol2'
Preparing input files

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

`REAL300000078483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078483 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 13, 13, 13, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 13, 45, 45, 90, 90, 45, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 268
rigid atoms, others: [1, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 282
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078483 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 7, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 67, 67, 67, 13, 13, 13, 5, 1, 1, 2, 2, 1, 45, 45, 45, 67, 67, 67, 67, 67, 67, 67] 268
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 111
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078483 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078483
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078483/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078483
Building REAL300000078484
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078484'
/scratch/stefan/7769659/working/building/REAL300000078484 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078484

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078484/0 /scratch/stefan/7769659/working/building/REAL300000078484 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/410
`/scratch/stefan/7769659/working/3D/410' -> `0.mol2'
Preparing input files

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

`REAL300000078484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078484 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 2, 2, 1] 76
rigid atoms, others: [32, 33, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 37
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078484 none O=C([O-])C1=C2C(=CC=C1)CCC2=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 38, 38, 19] 76
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 35, 36, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31])
total number of confs: 106
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078484 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078484
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078484/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078484
Building REAL300000078485
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078485'
/scratch/stefan/7769659/working/building/REAL300000078485 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078485

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078485/0 /scratch/stefan/7769659/working/building/REAL300000078485 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/411
`/scratch/stefan/7769659/working/3D/411' -> `0.mol2'
Preparing input files

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

`REAL300000078485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078485 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 27, 27, 27, 27, 27, 27, 27, 1, 1, 3, 3, 3, 3, 1, 1, 6, 20, 27, 27, 54, 54, 27, 1, 1, 3, 3] 108
rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 39, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 185
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078485 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 9, 23, 23, 23, 27, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 1, 3, 3, 8, 23, 27, 27, 54, 54, 27, 3, 3, 1, 1] 108
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: 182
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078485 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 23, 21, 27, 27, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 27, 27, 27, 27, 27, 21, 7, 1, 1, 2, 2, 1, 27, 27, 27, 27] 108
rigid atoms, others: [34, 35, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39, 40, 41, 42])
total number of confs: 85
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078485 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078485
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078485/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078485
Building REAL300000078486
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078486'
/scratch/stefan/7769659/working/building/REAL300000078486 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078486

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078486/0 /scratch/stefan/7769659/working/building/REAL300000078486 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/412
`/scratch/stefan/7769659/working/3D/412' -> `0.mol2'
Preparing input files

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

`REAL300000078486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078486 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [11, 1, 11, 11, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 15, 35, 35, 70, 70, 35, 1, 1, 1] 140
rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 215
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078486 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 35, 35, 35, 35, 15, 15, 15, 7, 1, 1, 2, 2, 1, 35, 35, 35] 140
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34])
total number of confs: 61
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078486 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078486
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078486/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078486
Building REAL300000078487
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078487'
/scratch/stefan/7769659/working/building/REAL300000078487 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078487

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078487/0 /scratch/stefan/7769659/working/building/REAL300000078487 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/413
`/scratch/stefan/7769659/working/3D/413' -> `0.mol2'
Preparing input files

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

`REAL300000078487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078487 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 14, 5, 1, 1, 2, 2, 1, 18] 72
rigid atoms, others: [32, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 36
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078487 none O=C([O-])C1=CC=C2NC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 6, 6, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 6, 9, 18, 18, 36, 36, 18, 1] 72
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 36] set([0, 32, 2, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31])
total number of confs: 115
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078487 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078487
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078487/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078487
Building REAL300000078488
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078488'
/scratch/stefan/7769659/working/building/REAL300000078488 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078488

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078488/0 /scratch/stefan/7769659/working/building/REAL300000078488 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/414
`/scratch/stefan/7769659/working/3D/414' -> `0.mol2'
Preparing input files

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

`REAL300000078488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078488 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 18, 7, 1, 1, 2, 2, 1, 29] 116
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 28, 29, 31])
total number of confs: 55
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078488 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 2, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 8, 18, 29, 29, 58, 58, 29, 1] 116
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 181
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078488 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078488
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078488/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078488
Building REAL300000078489
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078489'
/scratch/stefan/7769659/working/building/REAL300000078489 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078489

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078489/0 /scratch/stefan/7769659/working/building/REAL300000078489 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/415
`/scratch/stefan/7769659/working/3D/415' -> `0.mol2'
Preparing input files

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

`REAL300000078489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078489 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
336  conformations in input
total number of sets (complete confs): 336
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 24, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 24, 6, 1, 1, 2, 2, 1, 42, 84] 336
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33])
total number of confs: 159
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078489 none O=C([O-])C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
336  conformations in input
total number of sets (complete confs): 336
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 12, 42, 42, 84, 84, 42, 1, 2] 336
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33])
total number of confs: 248
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078489 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078489
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078489/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078489
Building REAL300000078490
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078490'
/scratch/stefan/7769659/working/building/REAL300000078490 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078490

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078490/0 /scratch/stefan/7769659/working/building/REAL300000078490 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/416
`/scratch/stefan/7769659/working/3D/416' -> `0.mol2'
Preparing input files

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

`REAL300000078490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078490 none CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 44, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 20, 7, 1, 1, 2, 2, 1, 44] 176
rigid atoms, others: [34, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
total number of confs: 70
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078490 none CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 16, 17, 16, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 16, 44, 44, 88, 88, 44, 1] 176
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 272
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078490 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078490
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078490/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078490
Building REAL300000078491
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078491'
/scratch/stefan/7769659/working/building/REAL300000078491 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078491

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078491/0 /scratch/stefan/7769659/working/building/REAL300000078491 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/417
`/scratch/stefan/7769659/working/3D/417' -> `0.mol2'
Preparing input files

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

`REAL300000078491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078491 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 24, 7, 1, 1, 2, 2, 1, 67] 268
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 26, 27, 29])
total number of confs: 101
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078491 none O=C([O-])C1=C(Cl)SC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 26, 26, 25, 67, 67, 67, 67, 67, 67, 67, 1, 12, 26, 67, 67, 134, 134, 67, 1] 268
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 400
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078491 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078491
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078491/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078491
Building REAL300000078492
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078492'
/scratch/stefan/7769659/working/building/REAL300000078492 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078492

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078492/0 /scratch/stefan/7769659/working/building/REAL300000078492 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/418
`/scratch/stefan/7769659/working/3D/418' -> `0.mol2'
Preparing input files

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

`REAL300000078492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078492 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [8, 1, 8, 8, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 13, 30, 31, 62, 62, 31, 1, 1, 1, 2, 2, 2] 124
rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 197
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078492 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 31, 31, 16, 16, 31, 31, 31, 31, 31, 16, 16, 16, 7, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 31] 124
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 127
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078492 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078492
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078492/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078492
Building REAL300000078493
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078493'
/scratch/stefan/7769659/working/building/REAL300000078493 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078493

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078493/0 /scratch/stefan/7769659/working/building/REAL300000078493 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/419
`/scratch/stefan/7769659/working/3D/419' -> `0.mol2'
Preparing input files

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

`REAL300000078493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078493 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [21, 21, 21, 21, 21, 15, 21, 21, 21, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 11, 7, 1, 1, 2, 2, 1] 84
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 29, 30])
total number of confs: 59
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078493 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 1, 1, 6, 8, 21, 21, 42, 42, 21] 84
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 129
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078493 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078493
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078493/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078493
Building REAL300000078494
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078494'
/scratch/stefan/7769659/working/building/REAL300000078494 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078494

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078494/0 /scratch/stefan/7769659/working/building/REAL300000078494 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/420
`/scratch/stefan/7769659/working/3D/420' -> `0.mol2'
Preparing input files

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

`REAL300000078494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078494 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 19, 5, 1, 1, 2, 2, 1] 124
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 53
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078494 none CN1N=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 6, 13, 31, 31, 62, 62, 31] 124
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 195
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078494 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078494
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078494/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078494
Building REAL300000078495
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078495'
/scratch/stefan/7769659/working/building/REAL300000078495 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078495

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078495/0 /scratch/stefan/7769659/working/building/REAL300000078495 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/421
`/scratch/stefan/7769659/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)O2)=CC=C1O)

`REAL300000078495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078495 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
536  conformations in input
total number of sets (complete confs): 536
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 17, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 11, 11, 11, 11, 11, 1, 1, 5, 11, 27, 27, 54, 54, 27, 11, 11, 22] 536
rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 218
number of broken/clashed sets: 134
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078495 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
536  conformations in input
total number of sets (complete confs): 536
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 28, 28, 28, 67, 67, 67, 67, 67, 67, 67, 11, 1, 1, 1, 1, 1, 11, 11, 18, 28, 67, 67, 134, 134, 67, 1, 1, 2] 536
rigid atoms, others: [1, 3, 4, 5, 6, 39, 27, 24, 25, 26, 38, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40])
total number of confs: 402
number of broken/clashed sets: 134
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078495 none O=C([O-])C1=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
536  conformations in input
total number of sets (complete confs): 536
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 27, 27, 27, 27, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 27, 67, 67, 67, 67, 67, 27, 27, 19, 5, 1, 1, 2, 2, 1, 67, 67, 134] 536
rigid atoms, others: [33, 34, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39, 40])
total number of confs: 236
number of broken/clashed sets: 134
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078495 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078495
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078495/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078495
Building REAL300000078496
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078496'
/scratch/stefan/7769659/working/building/REAL300000078496 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078496

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078496/0 /scratch/stefan/7769659/working/building/REAL300000078496 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/422
`/scratch/stefan/7769659/working/3D/422' -> `0.mol2'
Preparing input files

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

`REAL300000078496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078496 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [28, 28, 28, 28, 28, 28, 28, 28, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 20, 5, 1, 1, 2, 2, 1] 112
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 46
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078496 none CN1C=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 2, 2, 1, 1, 1, 6, 6, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 6, 13, 28, 28, 56, 56, 28] 112
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 25, 26] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 182
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078496 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078496
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078496/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078496
Building REAL300000078497
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078497'
/scratch/stefan/7769659/working/building/REAL300000078497 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078497

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078497/0 /scratch/stefan/7769659/working/building/REAL300000078497 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/423
`/scratch/stefan/7769659/working/3D/423' -> `0.mol2'
Preparing input files

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

`REAL300000078497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078497 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 5, 1, 1, 2, 2, 1] 148
rigid atoms, others: [36, 37, 40, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 59
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078497 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 14, 14, 14, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 14, 36, 37, 74, 74, 37] 148
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 33, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 237
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078497 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078497
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078497/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078497
Building REAL300000078498
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078498'
/scratch/stefan/7769659/working/building/REAL300000078498 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078498

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078498/0 /scratch/stefan/7769659/working/building/REAL300000078498 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/424
`/scratch/stefan/7769659/working/3D/424' -> `0.mol2'
Preparing input files

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

`REAL300000078498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078498 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 33, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 33, 7, 1, 1, 2, 2, 1] 236
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 98
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078498 none CC1=C(C(=O)[O-])C=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 18, 18, 18, 59, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2, 1, 6, 18, 59, 59, 118, 118, 59] 236
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 349
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078498 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078498
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078498/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078498
Building REAL300000078499
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078499'
/scratch/stefan/7769659/working/building/REAL300000078499 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078499

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078499/0 /scratch/stefan/7769659/working/building/REAL300000078499 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/425
`/scratch/stefan/7769659/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)C=C1)

`REAL300000078499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078499 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 1, 7, 7, 7, 7, 1, 1, 5, 15, 37, 37, 74, 74, 37, 7, 7] 268
rigid atoms, others: [6, 7, 8, 9, 10, 11, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 248
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078499 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 40, 40, 40, 67, 67, 67, 67, 67, 67, 67, 8, 1, 1, 1, 1, 8, 8, 22, 40, 67, 67, 134, 134, 67, 1, 1] 268
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: 422
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078499 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 65, 67, 65, 67, 67, 37, 37, 37, 37, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 37, 67, 67, 67, 67, 37, 37, 23, 6, 1, 1, 2, 2, 1, 67, 67] 268
rigid atoms, others: [33, 34, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38, 39])
total number of confs: 135
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078499 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078499
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078499/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078499
Building REAL300000078500
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078500'
/scratch/stefan/7769659/working/building/REAL300000078500 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078500

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078500/0 /scratch/stefan/7769659/working/building/REAL300000078500 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/426
`/scratch/stefan/7769659/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)=C1)

`REAL300000078500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078500 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 1, 11, 11, 11, 11, 1, 1, 5, 9, 23, 23, 46, 46, 23, 11] 268
rigid atoms, others: [7, 8, 9, 10, 11, 12, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 146
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078500 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 27, 27, 27, 67, 67, 67, 67, 67, 67, 67, 11, 1, 1, 1, 1, 11, 11, 19, 27, 67, 67, 134, 134, 67, 1] 268
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 396
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078500 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 23, 23, 23, 23, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 67, 67, 67, 67, 23, 23, 17, 5, 1, 1, 2, 2, 1, 67] 268
rigid atoms, others: [34, 35, 38, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 104
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078500 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078500
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078500/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078500
Building REAL300000078501
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078501'
/scratch/stefan/7769659/working/building/REAL300000078501 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078501

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078501/0 /scratch/stefan/7769659/working/building/REAL300000078501 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/427
`/scratch/stefan/7769659/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)S1)

`REAL300000078501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078501 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [50, 31, 31, 31, 31, 31, 32, 32, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 15, 7, 1, 1, 2, 2, 1] 200
rigid atoms, others: [32, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 172
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078501 none CCC1=CC(C(=O)[O-])=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 1, 7, 7, 7, 7, 7, 1, 5, 11, 31, 31, 62, 62, 31] 200
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 22, 28] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 209
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078501 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078501
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078501/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078501
Building REAL300000078502
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078502'
/scratch/stefan/7769659/working/building/REAL300000078502 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078502

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078502/0 /scratch/stefan/7769659/working/building/REAL300000078502 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/428
`/scratch/stefan/7769659/working/3D/428' -> `0.mol2'
Preparing input files

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

`REAL300000078502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078502 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 19, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 19, 6, 1, 1, 2, 2, 1] 268
rigid atoms, others: [32, 33, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 94
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078502 none COC1=CC=C(C(=O)[O-])C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 67, 67, 67, 67, 67, 67, 67, 4, 4, 4, 1, 1, 1, 11, 27, 67, 67, 134, 134, 67] 268
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 410
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078502 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078502
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078502/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078502
Building REAL300000078503
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078503'
/scratch/stefan/7769659/working/building/REAL300000078503 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078503

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078503/0 /scratch/stefan/7769659/working/building/REAL300000078503 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/429
`/scratch/stefan/7769659/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1)

`REAL300000078503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078503 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 14, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 5, 1, 1, 2, 2, 1, 19] 76
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
total number of confs: 37
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078503 none O=C([O-])C1=CC=C2SC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 14, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 6, 6, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 6, 10, 19, 19, 38, 38, 19, 1] 76
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26, 27] set([0, 32, 2, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31])
total number of confs: 123
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078503 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078503
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078503/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078503
Building REAL300000078504
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078504'
/scratch/stefan/7769659/working/building/REAL300000078504 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078504

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078504/0 /scratch/stefan/7769659/working/building/REAL300000078504 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/430
`/scratch/stefan/7769659/working/3D/430' -> `0.mol2'
Preparing input files

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

`REAL300000078504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078504 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 2, 2, 1, 14] 56
rigid atoms, others: [33, 34, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38])
total number of confs: 29
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078504 none O=C([O-])C1=CN=C2CCCC(=NNC(=O)C3=CC=C(O)C(O)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
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, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 28, 28, 14, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38] set([32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 80
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078504 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078504
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078504/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078504
Building REAL300000078505
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078505'
/scratch/stefan/7769659/working/building/REAL300000078505 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078505

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078505/0 /scratch/stefan/7769659/working/building/REAL300000078505 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/431
`/scratch/stefan/7769659/working/3D/431' -> `0.mol2'
Preparing input files

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

`REAL300000078505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078505 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [47, 47, 47, 47, 47, 47, 47, 47, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 23, 7, 1, 1, 2, 2, 1, 47] 188
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 32, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 75
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078505 none O=C([O-])C1=CC=C(Br)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 11, 25, 47, 45, 94, 94, 47, 1] 188
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 291
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078505 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078505
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078505/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078505
Building REAL300000078506
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078506'
/scratch/stefan/7769659/working/building/REAL300000078506 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078506

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078506/0 /scratch/stefan/7769659/working/building/REAL300000078506 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/432
`/scratch/stefan/7769659/working/3D/432' -> `0.mol2'
Preparing input files

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

`REAL300000078506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078506 none CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [17, 17, 17, 17, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 1, 1, 2, 2, 1, 17] 68
rigid atoms, others: [34, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35])
total number of confs: 37
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078506 none CC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 1, 2, 2, 2, 1, 1, 6, 8, 17, 17, 34, 34, 17, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 18, 19, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078506 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078506
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078506/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078506
Building REAL300000078507
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078507'
/scratch/stefan/7769659/working/building/REAL300000078507 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078507

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078507/0 /scratch/stefan/7769659/working/building/REAL300000078507 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/433
`/scratch/stefan/7769659/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1C(=O)[O-])

`REAL300000078507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078507 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 42, 42, 42, 21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 67, 67, 67, 67, 67, 42, 21, 5, 1, 1, 2, 2, 1, 42, 42] 268
rigid atoms, others: [34, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36])
total number of confs: 226
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078507 none COC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 6, 11, 42, 42, 84, 84, 42, 1, 1] 268
rigid atoms, others: [1, 2, 3, 4, 5, 35, 18, 19, 20, 21, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 253
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078507 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078507
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078507/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078507
Building REAL300000078508
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078508'
/scratch/stefan/7769659/working/building/REAL300000078508 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078508

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078508/0 /scratch/stefan/7769659/working/building/REAL300000078508 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/434
`/scratch/stefan/7769659/working/3D/434' -> `0.mol2'
Preparing input files

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

`REAL300000078508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078508 none O=C([O-])C1=CC(F)=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 15, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 15, 22, 22, 22, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 15, 5, 1, 1, 2, 2, 1, 22] 88
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 32, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 74
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078508 none O=C([O-])C1=CC(F)=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 15, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 6, 6, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 14, 22, 22, 44, 44, 22, 1] 88
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 145
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078508 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078508
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078508/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078508
Building REAL300000078509
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078509'
/scratch/stefan/7769659/working/building/REAL300000078509 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078509

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078509/0 /scratch/stefan/7769659/working/building/REAL300000078509 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/435
`/scratch/stefan/7769659/working/3D/435' -> `0.mol2'
Preparing input files

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

`REAL300000078509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078509 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
220  conformations in input
total number of sets (complete confs): 220
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 30, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 30, 7, 1, 1, 2, 2, 1, 55] 220
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33])
total number of confs: 90
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078509 none CC1=C(C(=O)[O-])NC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
220  conformations in input
total number of sets (complete confs): 220
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 16, 17, 16, 55, 55, 55, 55, 55, 55, 55, 1, 2, 2, 2, 1, 6, 16, 55, 55, 110, 110, 55, 1] 220
rigid atoms, others: [0, 1, 2, 3, 33, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 327
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078509 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078509
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078509/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078509
Building REAL300000078510
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078510'
/scratch/stefan/7769659/working/building/REAL300000078510 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078510

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078510/0 /scratch/stefan/7769659/working/building/REAL300000078510 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/436
`/scratch/stefan/7769659/working/3D/436' -> `0.mol2'
Preparing input files

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

`REAL300000078510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078510 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
344  conformations in input
total number of sets (complete confs): 344
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 20, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 86, 20, 6, 1, 1, 2, 2, 1, 43] 344
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 30, 31, 33])
total number of confs: 152
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078510 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 6, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
344  conformations in input
total number of sets (complete confs): 344
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 43, 43, 43, 43, 43, 43, 43, 1, 1, 2, 10, 20, 42, 43, 86, 86, 43, 1] 344
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 33] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 269
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078510 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078510/1 /scratch/stefan/7769659/working/building/REAL300000078510 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/437
`/scratch/stefan/7769659/working/3D/437' -> `1.mol2'
Preparing input files

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

`REAL300000078510.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078510/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078510 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 13, 5, 1, 1, 2, 2, 1, 17] 68
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 32, 23, 24, 25, 26, 29, 30])
total number of confs: 35
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078510 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 17, 1, 12, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 1, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 8, 17, 17, 34, 34, 17, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 23, 24] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 103
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078510 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078510
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078510/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078510/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078510
Building REAL300000078511
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078511'
/scratch/stefan/7769659/working/building/REAL300000078511 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078511

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078511/0 /scratch/stefan/7769659/working/building/REAL300000078511 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/438
`/scratch/stefan/7769659/working/3D/438' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)O1)

`REAL300000078511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078511 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 1, 1, 10, 10, 11, 3, 3, 1, 1, 8, 16, 33, 33, 66, 66, 33, 1, 1] 268
rigid atoms, others: [33, 34, 43, 7, 8, 9, 10, 11, 12, 13, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 225
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078511 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 34, 34, 44, 44, 44, 67, 67, 67, 67, 67, 67, 67, 10, 10, 1, 1, 1, 8, 8, 11, 11, 34, 44, 67, 67, 134, 134, 67, 10, 10] 268
rigid atoms, others: [1, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 442
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078511 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 38, 33, 29, 28, 33, 33, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 67, 67, 67, 38, 38, 33, 33, 15, 5, 1, 1, 2, 2, 1, 33, 33] 268
rigid atoms, others: [37, 38, 41, 16, 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, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 42, 43])
total number of confs: 152
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078511 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078511
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078511/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078511
Building REAL300000078512
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078512'
/scratch/stefan/7769659/working/building/REAL300000078512 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078512

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078512/0 /scratch/stefan/7769659/working/building/REAL300000078512 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/439
`/scratch/stefan/7769659/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1O)

`REAL300000078512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078512 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
432  conformations in input
total number of sets (complete confs): 432
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 25, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 25, 5, 1, 1, 2, 2, 1, 108] 432
rigid atoms, others: [34, 35, 38, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39])
total number of confs: 184
number of broken/clashed sets: 108
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078512 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
432  conformations in input
total number of sets (complete confs): 432
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 10, 23, 54, 54, 108, 108, 54, 2] 432
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 335
number of broken/clashed sets: 108
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078512 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078512
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078512/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078512
Building REAL300000078513
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078513'
/scratch/stefan/7769659/working/building/REAL300000078513 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078513

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078513/0 /scratch/stefan/7769659/working/building/REAL300000078513 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/440
`/scratch/stefan/7769659/working/3D/440' -> `0.mol2'
Preparing input files

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

`REAL300000078513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078513 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 6, 10, 29, 29, 58, 58, 29, 1, 1, 3] 268
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 44, 43, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 194
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078513 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 9, 16, 41, 42, 84, 84, 42, 3, 3, 1] 268
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 45, 28, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 274
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078513 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 42, 42, 42, 42, 42, 29, 29, 29, 25, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 42, 67, 67, 42, 42, 42, 29, 29, 18, 5, 1, 1, 2, 2, 1, 29, 29, 42] 268
rigid atoms, others: [38, 39, 42, 16, 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, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 43, 44, 45])
total number of confs: 242
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078513 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078513
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078513/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078513
Building REAL300000078514
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078514'
/scratch/stefan/7769659/working/building/REAL300000078514 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078514

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078514/0 /scratch/stefan/7769659/working/building/REAL300000078514 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/441
`/scratch/stefan/7769659/working/3D/441' -> `0.mol2'
Preparing input files

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

`REAL300000078514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078514 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 16, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 14, 5, 1, 1, 2, 2, 1, 20] 80
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 26, 27, 29])
total number of confs: 40
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078514 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 16, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 4, 4, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 4, 11, 20, 20, 40, 40, 20, 1] 80
rigid atoms, others: [1, 3, 4, 5, 18, 19, 20, 21, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 131
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078514 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078514
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078514/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078514
Building REAL300000078515
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078515'
/scratch/stefan/7769659/working/building/REAL300000078515 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078515

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078515/0 /scratch/stefan/7769659/working/building/REAL300000078515 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/442
`/scratch/stefan/7769659/working/3D/442' -> `0.mol2'
Preparing input files

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

`REAL300000078515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078515 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [21, 21, 21, 21, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 13, 5, 1, 1, 2, 2, 1, 21, 21] 84
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 25, 26, 28, 29])
total number of confs: 42
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078515 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 1, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 5, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 11, 21, 21, 42, 42, 21, 1, 1] 84
rigid atoms, others: [1, 3, 4, 5, 18, 19, 20, 28, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 136
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078515 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078515
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078515/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078515
Building REAL300000078516
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078516'
/scratch/stefan/7769659/working/building/REAL300000078516 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078516

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078516/0 /scratch/stefan/7769659/working/building/REAL300000078516 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/443
`/scratch/stefan/7769659/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CS1)

`REAL300000078516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078516 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [32, 32, 32, 32, 32, 22, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 22, 5, 1, 1, 2, 2, 1, 32] 128
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 26, 27, 29])
total number of confs: 52
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078516 none O=C([O-])C1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 14, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 6, 6, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 13, 32, 32, 64, 64, 32, 1] 128
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 198
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078516 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078516
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078516/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078516
Building REAL300000078517
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078517'
/scratch/stefan/7769659/working/building/REAL300000078517 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078517

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078517/0 /scratch/stefan/7769659/working/building/REAL300000078517 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/444
`/scratch/stefan/7769659/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-])

`REAL300000078517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078517 none CCOC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 11, 11, 11, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 67, 67, 67, 22, 22, 22, 22, 22, 11, 5, 5, 1, 1, 2, 2, 1, 11, 11, 67, 67] 268
rigid atoms, others: [35, 36, 39, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 40, 41, 42, 43])
total number of confs: 218
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078517 none CCOC1=CC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 16, 16, 16, 8, 8, 8, 8, 8, 1, 4, 4, 11, 11, 22, 22, 11, 1, 1, 16, 16] 268
rigid atoms, others: [32, 2, 3, 4, 5, 6, 40, 41, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 42, 43])
total number of confs: 132
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078517 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078517
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078517/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078517
Building REAL300000078518
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078518'
/scratch/stefan/7769659/working/building/REAL300000078518 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078518

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078518/0 /scratch/stefan/7769659/working/building/REAL300000078518 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/445
`/scratch/stefan/7769659/working/3D/445' -> `0.mol2'
Preparing input files

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

`REAL300000078518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078518 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 25, 25, 25, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 18, 25, 59, 59, 118, 118, 59] 236
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 362
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078518 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 5, 11, 20, 20, 40, 40, 20] 236
rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 36] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 147
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078518 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
236  conformations in input
total number of sets (complete confs): 236
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 59, 59, 59, 59, 59, 20, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 20, 13, 5, 1, 1, 2, 2, 1] 236
rigid atoms, others: [39, 40, 43, 17, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 147
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078518 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078518
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078518/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078518
Building REAL300000078519
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078519'
/scratch/stefan/7769659/working/building/REAL300000078519 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078519

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078519/0 /scratch/stefan/7769659/working/building/REAL300000078519 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/446
`/scratch/stefan/7769659/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-])

`REAL300000078519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078519 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
232  conformations in input
total number of sets (complete confs): 232
using faster count positions algorithm for large data
unique positions, atoms: [58, 34, 34, 34, 34, 34, 34, 26, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 58, 58, 58, 58, 58, 34, 34, 34, 34, 34, 26, 5, 1, 1, 2, 2, 1] 232
rigid atoms, others: [35, 36, 39, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 200
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078519 none COC1=CC=C(C)C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
232  conformations in input
total number of sets (complete confs): 232
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 34, 34, 34, 34, 34, 34, 34, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 3, 14, 34, 34, 68, 68, 34] 232
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 216
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078519 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078519
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078519/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078519
Building REAL300000078520
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078520'
/scratch/stefan/7769659/working/building/REAL300000078520 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078520

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078520/0 /scratch/stefan/7769659/working/building/REAL300000078520 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/447
`/scratch/stefan/7769659/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-])

`REAL300000078520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078520 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 5, 1, 1, 2, 2, 1] 76
rigid atoms, others: [35, 36, 39, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 41
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078520 none CN1C2=CC=C(F)C=C2C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 6, 10, 19, 19, 38, 38, 19] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 23, 24, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 131
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078520 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078520
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078520/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078520
Building REAL300000078521
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078521'
/scratch/stefan/7769659/working/building/REAL300000078521 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078521

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078521/0 /scratch/stefan/7769659/working/building/REAL300000078521 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/448
`/scratch/stefan/7769659/working/3D/448' -> `0.mol2'
Preparing input files

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

`REAL300000078521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078521 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 33, 33, 66, 66, 33, 1, 1, 1, 1] 132
rigid atoms, others: [1, 35, 36, 37, 38, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 201
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078521 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [21, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 5, 1, 1, 2, 2, 1, 33, 33, 33, 33] 132
rigid atoms, others: [34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078521 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078521
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078521/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078521
Building REAL300000078522
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078522'
/scratch/stefan/7769659/working/building/REAL300000078522 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078522

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078522/0 /scratch/stefan/7769659/working/building/REAL300000078522 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/449
`/scratch/stefan/7769659/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1)

`REAL300000078522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078522 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 63, 51, 23, 23, 23, 23, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 67, 67, 51, 51, 23, 23, 17, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [32, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 236
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078522 none O=C([O-])CCC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [20, 16, 14, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 1, 16, 16, 9, 9, 1, 1, 4, 10, 23, 23, 46, 46, 23] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 216
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078522 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078522
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078522/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078522
Building REAL300000078523
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078523'
/scratch/stefan/7769659/working/building/REAL300000078523 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078523

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078523/0 /scratch/stefan/7769659/working/building/REAL300000078523 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/450
`/scratch/stefan/7769659/working/3D/450' -> `0.mol2'
Preparing input files

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

`REAL300000078523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078523 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 17, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 14, 5, 1, 1, 2, 2, 1, 20] 80
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 26, 27, 29])
total number of confs: 40
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078523 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 14, 1, 17, 1, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 4, 4, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 4, 11, 20, 20, 40, 40, 20, 1] 80
rigid atoms, others: [1, 3, 4, 5, 18, 19, 20, 21, 29] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 131
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078523 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078523
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078523/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078523
Building REAL300000078524
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078524'
/scratch/stefan/7769659/working/building/REAL300000078524 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078524

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078524/0 /scratch/stefan/7769659/working/building/REAL300000078524 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/451
`/scratch/stefan/7769659/working/3D/451' -> `0.mol2'
Preparing input files

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

`REAL300000078524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078524 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [33, 33, 33, 33, 33, 33, 33, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 15, 7, 1, 1, 2, 2, 1, 33, 33, 33] 132
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36])
total number of confs: 63
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078524 none O=C([O-])C1=C2NC=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 6, 10, 33, 33, 66, 66, 33, 1, 1, 1] 132
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26, 36] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 190
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078524 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078524
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078524/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078524
Building REAL300000078525
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078525'
/scratch/stefan/7769659/working/building/REAL300000078525 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078525

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078525/0 /scratch/stefan/7769659/working/building/REAL300000078525 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/452
`/scratch/stefan/7769659/working/3D/452' -> `0.mol2'
Preparing input files

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

`REAL300000078525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078525 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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]
2  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 26, 26, 13, 1, 1, 1, 1, 1] 52
rigid atoms, others: [1, 36, 37, 38, 39, 40, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 83
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078525 none CC(=NNC(=O)C1=CC=C(O)C(O)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 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]
2  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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 5, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13] 52
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 31
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078525 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078525
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078525/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078525
Building REAL300000078526
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078526'
/scratch/stefan/7769659/working/building/REAL300000078526 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078526

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078526/0 /scratch/stefan/7769659/working/building/REAL300000078526 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/453
`/scratch/stefan/7769659/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=C2O1)

`REAL300000078526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078526 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 16, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 16, 5, 1, 1, 2, 2, 1, 29, 29] 116
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35])
total number of confs: 54
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078526 none O=C([O-])C1=CC2=CC(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 8, 17, 29, 29, 58, 58, 29, 1, 1] 116
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 184
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078526 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078526
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078526/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078526
Building REAL300000078527
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078527'
/scratch/stefan/7769659/working/building/REAL300000078527 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078527

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078527/0 /scratch/stefan/7769659/working/building/REAL300000078527 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/454
`/scratch/stefan/7769659/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=CN12)

`REAL300000078527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078527 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 19, 19, 19, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 5, 1, 1, 2, 2, 1, 19, 19, 19] 76
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34, 35])
total number of confs: 37
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078527 none O=C([O-])C1=CN=C2C(C=NNC(=O)C3=CC=C(O)C(O)=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 9, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 6, 10, 19, 19, 38, 38, 19, 1, 1, 1] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 21, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31])
total number of confs: 121
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078527 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078527
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078527/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078527
Building REAL300000078528
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078528'
/scratch/stefan/7769659/working/building/REAL300000078528 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078528

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078528/0 /scratch/stefan/7769659/working/building/REAL300000078528 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/455
`/scratch/stefan/7769659/working/3D/455' -> `0.mol2'
Preparing input files

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

`REAL300000078528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078528 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 5, 1, 1, 2, 2, 1] 60
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 33
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078528 none O=C([O-])C1=C(F)C=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 6, 15, 15, 30, 30, 15] 60
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 97
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078528 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078528
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078528/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078528
Building REAL300000078529
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078529'
/scratch/stefan/7769659/working/building/REAL300000078529 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078529

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078529/0 /scratch/stefan/7769659/working/building/REAL300000078529 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/456
`/scratch/stefan/7769659/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2=CC=C(O)C(O)=C2)O1)

`REAL300000078529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078529 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 29, 29, 29, 13, 13, 1, 1, 1, 1, 4, 6, 19, 19, 38, 38, 19] 268
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 174
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078529 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 22, 29, 29, 29, 29, 29, 29, 32, 32, 35, 35, 35, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 7, 7, 29, 29, 29, 29, 32, 35, 67, 67, 134, 134, 67] 268
rigid atoms, others: [1, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 404
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078529 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC(=O)C2=CC=C(O)C(O)=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 53, 36, 19, 19, 19, 19, 19, 19, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 53, 53, 19, 19, 19, 19, 11, 5, 1, 1, 2, 2, 1] 268
rigid atoms, others: [39, 40, 43, 18, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 183
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078529 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078529
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078529/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078529
Building REAL300000078530
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078530'
/scratch/stefan/7769659/working/building/REAL300000078530 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078530

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078530/0 /scratch/stefan/7769659/working/building/REAL300000078530 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/457
`/scratch/stefan/7769659/working/3D/457' -> `0.mol2'
Preparing input files

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

`REAL300000078530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078530 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 9, 5, 1, 1, 2, 2, 1] 44
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 27
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078530 none O=C([O-])C1=C(Br)C=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 11, 11, 22, 22, 11] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 69
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078530 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078530
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078530/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078530
Building REAL300000078531
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078531'
/scratch/stefan/7769659/working/building/REAL300000078531 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078531

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078531/0 /scratch/stefan/7769659/working/building/REAL300000078531 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/458
`/scratch/stefan/7769659/working/3D/458' -> `0.mol2'
Preparing input files

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

`REAL300000078531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078531 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [65, 46, 46, 46, 46, 46, 65, 46, 46, 46, 46, 46, 46, 48, 48, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 46, 65, 65, 65, 46, 46, 19, 7, 1, 1, 2, 2, 1] 268
rigid atoms, others: [40, 41, 44, 19, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43])
total number of confs: 155
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078531 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 15, 15, 15, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 3, 3, 3, 1, 1, 8, 15, 46, 46, 92, 92, 46] 268
rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 36, 37] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 278
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078531 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078531
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078531/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078531
Building REAL300000078532
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078532'
/scratch/stefan/7769659/working/building/REAL300000078532 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078532

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078532/0 /scratch/stefan/7769659/working/building/REAL300000078532 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/459
`/scratch/stefan/7769659/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C2=C(C=C1)OCO2)

`REAL300000078532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078532 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 9, 5, 1, 1, 2, 2, 1, 25, 25, 25, 25] 100
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35])
total number of confs: 47
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078532 none O=C([O-])C1=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C2=C(C=C1)OCO2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 1, 12, 5, 12, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 3, 1, 1, 1, 6, 6, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 6, 11, 25, 25, 50, 50, 25, 1, 1, 1, 1] 100
rigid atoms, others: [32, 1, 34, 3, 4, 5, 35, 33, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 161
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078532 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078532
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078532/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078532
Building REAL300000078533
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078533'
/scratch/stefan/7769659/working/building/REAL300000078533 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078533

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078533/0 /scratch/stefan/7769659/working/building/REAL300000078533 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/460
`/scratch/stefan/7769659/working/3D/460' -> `0.mol2'
Preparing input files

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

`REAL300000078533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078533 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 9, 5, 1, 1, 2, 2, 1, 17] 68
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 30, 31, 33])
total number of confs: 37
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078533 none N#CC1=CC=C(C(=O)[O-])C(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', '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, 11, 11, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 3, 3, 1, 1, 6, 6, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 8, 17, 17, 34, 34, 17, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 23, 24, 25] set([32, 7, 8, 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: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078533 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078533
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078533/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078533
Building REAL300000078534
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078534'
/scratch/stefan/7769659/working/building/REAL300000078534 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078534

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078534/0 /scratch/stefan/7769659/working/building/REAL300000078534 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/461
`/scratch/stefan/7769659/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1Cl)

`REAL300000078534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078534 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 54, 26, 13, 26, 26, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 67, 67, 26, 26, 9, 5, 1, 1, 2, 2, 1, 26] 268
rigid atoms, others: [32, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 36])
total number of confs: 202
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078534 none O=C([O-])COC1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [25, 22, 25, 7, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 22, 22, 1, 1, 6, 10, 26, 26, 52, 52, 26, 1] 268
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 36, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 233
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078534 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078534
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078534/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078534
Building REAL300000078535
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078535'
/scratch/stefan/7769659/working/building/REAL300000078535 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078535

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078535/0 /scratch/stefan/7769659/working/building/REAL300000078535 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/462
`/scratch/stefan/7769659/working/3D/462' -> `0.mol2'
Preparing input files

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

`REAL300000078535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078535 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
232  conformations in input
total number of sets (complete confs): 232
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 49, 30, 9, 30, 30, 9, 30, 30, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 58, 58, 49, 30, 30, 9, 5, 1, 1, 2, 2, 1, 30, 30] 232
rigid atoms, others: [34, 35, 38, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 39, 40])
total number of confs: 286
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078535 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC(=O)C2=CC=C(O)C(O)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
232  conformations in input
total number of sets (complete confs): 232
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 1, 1, 9, 9, 5, 1, 1, 6, 11, 30, 30, 60, 60, 30, 1, 1] 232
rigid atoms, others: [5, 39, 8, 9, 10, 11, 12, 40, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 216
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078535 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078535
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078535/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078535
Building REAL300000078536
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078536'
/scratch/stefan/7769659/working/building/REAL300000078536 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078536

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078536/0 /scratch/stefan/7769659/working/building/REAL300000078536 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/463
`/scratch/stefan/7769659/working/3D/463' -> `0.mol2'
Preparing input files

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

`REAL300000078536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078536 none CC1=NSC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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: [19, 19, 19, 19, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 14, 5, 1, 1, 2, 2, 1] 76
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 38
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078536 none CC1=NSC(C=NNC(=O)C2=CC=C(O)C(O)=C2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  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, 5, 5, 9, 9, 8, 19, 19, 19, 19, 19, 19, 19, 1, 1, 3, 3, 2, 2, 2, 5, 9, 19, 19, 38, 38, 19] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078536 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078536
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078536/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078536
Building REAL300000078537
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078537'
/scratch/stefan/7769659/working/building/REAL300000078537 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078537

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078537/0 /scratch/stefan/7769659/working/building/REAL300000078537 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/464
`/scratch/stefan/7769659/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C(F)=CC=C2S1)

`REAL300000078537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078537 none O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 24, 7, 1, 1, 2, 2, 1, 46, 46] 184
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35])
total number of confs: 76
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078537 none O=C([O-])C1=CC2=C(C=NNC(=O)C3=CC=C(O)C(O)=C3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 21, 21, 21, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 11, 21, 46, 46, 92, 92, 46, 1, 1] 184
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 283
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078537 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078537
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078537/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078537
Building REAL300000078538
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078538'
/scratch/stefan/7769659/working/building/REAL300000078538 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078538

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078538/0 /scratch/stefan/7769659/working/building/REAL300000078538 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/465
`/scratch/stefan/7769659/working/3D/465' -> `0.mol2'
Preparing input files

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

`REAL300000078538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078538 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 17, 7, 1, 1, 2, 2, 1] 180
rigid atoms, others: [32, 33, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 74
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078538 none COC1=CC(C(=O)[O-])=CC=C1C=NNC(=O)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 1, 10, 16, 45, 45, 90, 90, 45] 180
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 270
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078538 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078538
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078538/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078538
Building REAL300000078539
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078539'
/scratch/stefan/7769659/working/building/REAL300000078539 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078539

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078539/0 /scratch/stefan/7769659/working/building/REAL300000078539 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/466
`/scratch/stefan/7769659/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1)C1=CC=C(O)C(O)=C1)

`REAL300000078539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078539 none O=C(NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 1, 12, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 18, 18, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 27, 67, 67, 67, 67, 67, 67, 67, 27, 18, 1, 1, 1, 1, 11, 11, 67, 67, 134, 134, 67] 268
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 400
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078539 none O=C(NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 1, 12, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 4, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 11, 1, 1, 10, 31, 31, 31, 31, 31, 31, 31, 10, 4, 11, 11, 11, 11, 1, 1, 31, 31, 62, 62, 31] 268
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 17, 18] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 231
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078539 none O=C(NN=CC1=NN([C@H]2C[C@H](C(=O)[O-])C2)C=C1)C1=CC=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 8, 1, 1, 8, 8, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 1, 12, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 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]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 17, 17, 31, 31, 31, 67, 67, 67, 67, 67, 67, 67, 67, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 67, 67, 67, 67, 31, 31, 1, 1, 2, 2, 1] 268
rigid atoms, others: [1, 35, 36, 39, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 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, 37, 38])
total number of confs: 156
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078539 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078539
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078539/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078539
Building REAL300000078540
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078540'
/scratch/stefan/7769659/working/building/REAL300000078540 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078540

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078540/0 /scratch/stefan/7769659/working/building/REAL300000078540 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/467
`/scratch/stefan/7769659/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078540 none O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 69, 23, 23, 23, 12, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 23, 23, 23, 23, 9, 1, 1] 116
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])
total number of confs: 361
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078540 none O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [73, 46, 73, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 10, 23, 23, 23, 46, 46, 1, 1, 1, 1, 6, 23, 23] 116
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29])
total number of confs: 302
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078540 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078540/1 /scratch/stefan/7769659/working/building/REAL300000078540 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/468
`/scratch/stefan/7769659/working/3D/468' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078540.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078540/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078540 none O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 46, 19, 19, 19, 9, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 19, 19, 19, 19, 9, 1] 56
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 153
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078540 none O=C([O-])COC1=CC=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [35, 27, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 8, 19, 19, 19, 27, 27, 1, 1, 1, 1, 5, 19] 56
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28])
total number of confs: 160
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078540 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078540
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078540/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078540/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078540
Building REAL300000078541
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078541'
/scratch/stefan/7769659/working/building/REAL300000078541 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078541

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078541/0 /scratch/stefan/7769659/working/building/REAL300000078541 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/469
`/scratch/stefan/7769659/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-])

`REAL300000078541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078541 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 115, 197, 201, 201, 52, 52, 52, 26, 6, 1, 1, 26, 26, 197, 197] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 614
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078541 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 13, 26, 26, 26, 1, 1, 1, 1, 9, 41, 69, 69, 3, 3, 3, 1, 7, 26, 26, 1, 1, 41, 41] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 26, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33])
total number of confs: 299
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078541 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078541/1 /scratch/stefan/7769659/working/building/REAL300000078541 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/470
`/scratch/stefan/7769659/working/3D/470' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-])

`REAL300000078541.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078541/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078541 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 119, 201, 201, 201, 64, 64, 64, 31, 7, 1, 31, 31, 201, 201] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 627
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078541 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 15, 31, 31, 31, 1, 1, 1, 1, 9, 39, 73, 73, 4, 4, 4, 1, 10, 31, 1, 1, 39, 39] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 26, 29, 30] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31])
total number of confs: 330
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078541 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078541
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078541/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078541/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078541
Building REAL300000078542
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078542'
/scratch/stefan/7769659/working/building/REAL300000078542 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078542

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078542/0 /scratch/stefan/7769659/working/building/REAL300000078542 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/471
`/scratch/stefan/7769659/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)

`REAL300000078542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078542 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 106, 109, 50, 9, 9, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 106, 106, 40, 40, 9, 1, 1, 40, 40] 109
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 412
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078542 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [25, 17, 25, 3, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 40, 24, 40, 40, 40, 1, 1, 17, 17, 1, 1, 12, 40, 40, 1, 1] 109
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27])
total number of confs: 179
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078542 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078542/1 /scratch/stefan/7769659/working/building/REAL300000078542 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/472
`/scratch/stefan/7769659/working/3D/472' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)

`REAL300000078542.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078542/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078542 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 52, 36, 19, 36, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 84, 84, 36, 36, 9, 1, 36, 36] 84
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 27, 28])
total number of confs: 305
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078542 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [27, 16, 27, 4, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 24, 36, 36, 36, 1, 1, 16, 16, 1, 1, 11, 36, 1, 1] 84
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26])
total number of confs: 175
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078542 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078542
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078542/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078542/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078542
Building REAL300000078543
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078543'
/scratch/stefan/7769659/working/building/REAL300000078543 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078543

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078543/0 /scratch/stefan/7769659/working/building/REAL300000078543 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/473
`/scratch/stefan/7769659/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)

`REAL300000078543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078543 none O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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, 72, 41, 32, 6, 6, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 72, 72, 41, 41, 23, 23, 6, 1, 1, 23, 23] 72
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 294
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078543 none O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [24, 19, 24, 9, 3, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 13, 23, 23, 23, 1, 1, 19, 19, 9, 9, 1, 1, 7, 23, 23, 1, 1] 72
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30])
total number of confs: 158
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078543 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078543/1 /scratch/stefan/7769659/working/building/REAL300000078543 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/474
`/scratch/stefan/7769659/working/3D/474' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)

`REAL300000078543.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078543/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078543 none O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 36, 27, 18, 8, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 49, 49, 36, 36, 18, 18, 6, 1, 18, 18] 49
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078543 none O=C([O-])CCOC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [19, 16, 19, 8, 4, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 12, 18, 18, 18, 1, 1, 16, 16, 8, 8, 1, 1, 6, 18, 1, 1] 49
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 21, 26, 27, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078543 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078543
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078543/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078543/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078543
Building REAL300000078544
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078544'
/scratch/stefan/7769659/working/building/REAL300000078544 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078544

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078544/0 /scratch/stefan/7769659/working/building/REAL300000078544 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/475
`/scratch/stefan/7769659/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078544 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 64, 19, 19, 19, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 19, 19, 19, 8, 1, 1] 115
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27])
total number of confs: 336
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078544 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [77, 49, 77, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 8, 19, 19, 19, 49, 49, 1, 1, 1, 5, 19, 19] 115
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29])
total number of confs: 302
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078544 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078544/1 /scratch/stefan/7769659/working/building/REAL300000078544 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/476
`/scratch/stefan/7769659/working/3D/476' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078544.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078544/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078544 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 48, 18, 18, 18, 8, 18, 18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 18, 18, 18, 8, 1] 59
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27])
total number of confs: 167
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078544 none O=C([O-])COC1=CC=C(Br)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [36, 26, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 8, 18, 18, 18, 26, 26, 1, 1, 1, 5, 18] 59
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 169
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078544 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078544
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078544/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078544/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078544
Building REAL300000078545
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078545'
/scratch/stefan/7769659/working/building/REAL300000078545 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078545

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078545/0 /scratch/stefan/7769659/working/building/REAL300000078545 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/477
`/scratch/stefan/7769659/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C(=O)[O-])

`REAL300000078545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078545 none CC(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 127, 31, 31, 31, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 6, 1, 1, 31] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 555
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078545 none CC(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 18, 31, 31, 31, 1, 36, 54, 54, 36, 36, 36, 36, 1, 1, 1, 11, 31, 31, 1] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 272
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078545 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078545/1 /scratch/stefan/7769659/working/building/REAL300000078545 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/478
`/scratch/stefan/7769659/working/3D/478' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C(=O)[O-])

`REAL300000078545.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078545/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078545 none CC(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [173, 112, 37, 37, 37, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 173, 173, 173, 173, 173, 173, 173, 37, 37, 37, 9, 1, 37] 173
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 459
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078545 none CC(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [37, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 18, 37, 37, 37, 1, 37, 52, 52, 37, 37, 37, 37, 1, 1, 1, 11, 37, 1] 173
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 26, 27, 28, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 275
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078545 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078545
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078545/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078545/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078545
Building REAL300000078546
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078546'
/scratch/stefan/7769659/working/building/REAL300000078546 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078546

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078546/0 /scratch/stefan/7769659/working/building/REAL300000078546 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/479
`/scratch/stefan/7769659/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078546 none O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 168, 92, 36, 36, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 201, 201, 168, 168, 36, 36, 36, 8, 1, 1, 36] 201
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])
total number of confs: 652
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078546 none O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 37, 45, 24, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 36, 36, 23, 36, 36, 36, 1, 37, 37, 24, 24, 1, 1, 1, 12, 36, 36, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 290
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078546 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078546/1 /scratch/stefan/7769659/working/building/REAL300000078546 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/480
`/scratch/stefan/7769659/working/3D/480' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078546.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078546/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078546 none O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 123, 111, 69, 34, 34, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 127, 127, 111, 111, 34, 34, 34, 8, 1, 34] 127
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 375
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078546 none O=C([O-])CCOC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [42, 30, 38, 20, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 34, 34, 20, 34, 34, 34, 1, 30, 30, 20, 20, 1, 1, 1, 12, 34, 1] 127
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30])
total number of confs: 242
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078546 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078546
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078546/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078546/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078546
Building REAL300000078547
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078547'
/scratch/stefan/7769659/working/building/REAL300000078547 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078547

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078547/0 /scratch/stefan/7769659/working/building/REAL300000078547 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/481
`/scratch/stefan/7769659/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [19, 16, 19, 16, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 13, 20, 20, 20, 1, 16, 16, 16, 16, 6, 6, 1, 1, 1, 7, 20, 20, 1] 86
rigid atoms, others: [33, 34, 35, 39, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 94
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 16, 16, 16, 16, 16, 47, 47, 86, 86, 86, 76, 86, 86, 86, 16, 1, 1, 1, 1, 5, 5, 16, 16, 16, 47, 86, 86, 16] 86
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 219
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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, 86, 86, 86, 86, 86, 86, 48, 33, 20, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 86, 86, 86, 86, 48, 48, 20, 20, 20, 6, 1, 1, 20] 86
rigid atoms, others: [37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 168
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078547 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078547/1 /scratch/stefan/7769659/working/building/REAL300000078547 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/482
`/scratch/stefan/7769659/working/3D/482' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078547.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078547/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 11, 11, 10, 11, 11, 4, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 16, 24, 24, 24, 1, 11, 10, 11, 11, 4, 4, 1, 1, 1, 10, 24, 1] 56
rigid atoms, others: [33, 34, 35, 38, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 11, 29, 29, 56, 56, 56, 47, 56, 56, 56, 11, 1, 1, 1, 1, 6, 6, 11, 10, 11, 29, 56, 11] 56
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 147
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078547 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 33, 29, 24, 24, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 56, 56, 56, 56, 33, 33, 24, 24, 24, 7, 1, 24] 56
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38])
total number of confs: 94
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078547 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078547
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078547/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078547/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078547
Building REAL300000078548
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078548'
/scratch/stefan/7769659/working/building/REAL300000078548 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078548

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078548/0 /scratch/stefan/7769659/working/building/REAL300000078548 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/483
`/scratch/stefan/7769659/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1[N+](=O)[O-])

`REAL300000078548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078548 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 118, 45, 45, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 182, 182, 45, 45, 8, 1, 1, 45] 182
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 466
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078548 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 3, 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: [55, 34, 55, 7, 1, 1, 1, 1, 1, 1, 12, 12, 45, 45, 45, 23, 45, 45, 45, 1, 1, 1, 2, 2, 34, 34, 1, 1, 12, 45, 45, 1] 182
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30])
total number of confs: 308
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078548 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078548/1 /scratch/stefan/7769659/working/building/REAL300000078548 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/484
`/scratch/stefan/7769659/working/3D/484' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1[N+](=O)[O-])

`REAL300000078548.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078548/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078548 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 122, 46, 18, 46, 46, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 174, 174, 46, 46, 9, 1, 46] 174
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30])
total number of confs: 529
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078548 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [61, 38, 61, 7, 1, 1, 1, 1, 1, 1, 13, 13, 46, 46, 46, 22, 46, 46, 46, 1, 1, 1, 2, 2, 38, 38, 1, 1, 13, 46, 1] 174
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29])
total number of confs: 322
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078548 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078548
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078548/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078548/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078548
Building REAL300000078549
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078549'
/scratch/stefan/7769659/working/building/REAL300000078549 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078549

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078549/0 /scratch/stefan/7769659/working/building/REAL300000078549 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/485
`/scratch/stefan/7769659/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1)

`REAL300000078549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 37, 55, 55, 37, 13, 2, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 14, 23, 23, 23, 1, 1, 37, 37, 37, 37, 13, 13, 1, 1, 8, 23, 23, 1, 1, 37] 201
rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39])
total number of confs: 207
number of broken/clashed sets: 96
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 31, 37, 37, 37, 37, 112, 112, 201, 201, 201, 190, 201, 201, 201, 37, 37, 1, 2, 2, 2, 9, 9, 37, 37, 112, 201, 201, 36, 37, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 39, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 477
number of broken/clashed sets: 96
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 74, 27, 23, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 74, 74, 23, 23, 7, 1, 1, 23, 23, 201] 201
rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 398
number of broken/clashed sets: 96
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078549 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078549/1 /scratch/stefan/7769659/working/building/REAL300000078549 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/486
`/scratch/stefan/7769659/working/3D/486' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1)

`REAL300000078549.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078549/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', '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, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 50, 50, 33, 11, 3, 1, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 18, 32, 32, 32, 1, 1, 33, 33, 33, 33, 11, 11, 1, 1, 11, 32, 1, 1, 33] 184
rigid atoms, others: [32, 33, 36, 37, 9, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 38])
total number of confs: 214
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', '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, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 25, 33, 33, 33, 33, 110, 110, 184, 184, 184, 182, 184, 184, 184, 33, 33, 1, 2, 2, 2, 9, 9, 33, 33, 110, 184, 33, 33, 1] 184
rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 423
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078549 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', '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, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [184, 184, 184, 184, 184, 184, 184, 72, 37, 32, 18, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 184, 184, 184, 184, 72, 72, 32, 32, 9, 1, 32, 32, 184] 184
rigid atoms, others: [35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 418
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078549 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078549
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078549/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078549/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078549
Building REAL300000078550
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078550'
/scratch/stefan/7769659/working/building/REAL300000078550 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078550

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078550/0 /scratch/stefan/7769659/working/building/REAL300000078550 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/487
`/scratch/stefan/7769659/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=NNC3=S)=C2)=C1)

`REAL300000078550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=NNC3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 34, 35, 35, 12, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 18, 18, 18, 17, 18, 18, 18, 1, 35, 34, 35, 35, 12, 12, 1, 1, 1, 10, 18, 18, 1, 35] 201
rigid atoms, others: [32, 33, 34, 38, 9, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39])
total number of confs: 109
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=NNC3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 35, 35, 35, 35, 35, 125, 125, 201, 201, 201, 201, 201, 201, 201, 35, 1, 1, 1, 1, 9, 9, 35, 35, 35, 125, 201, 201, 35, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 440
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=NNC3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 52, 34, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 52, 52, 18, 18, 18, 6, 1, 1, 18, 201] 201
rigid atoms, others: [36, 37, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 314
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078550 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078550/1 /scratch/stefan/7769659/working/building/REAL300000078550 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/488
`/scratch/stefan/7769659/working/3D/488' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=N[N-]C3=S)=C2)=C1)

`REAL300000078550.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078550/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=N[N-]C3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 36, 35, 36, 36, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 17, 19, 19, 19, 1, 36, 35, 36, 36, 10, 10, 1, 1, 1, 10, 19, 1, 36] 181
rigid atoms, others: [32, 33, 34, 37, 9, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 38])
total number of confs: 114
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=N[N-]C3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 36, 36, 36, 36, 36, 116, 116, 181, 181, 181, 181, 181, 181, 181, 36, 1, 1, 1, 1, 9, 9, 36, 36, 36, 116, 181, 36, 1] 181
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 392
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078550 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NN3C(=O)C=N[N-]C3=S)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [181, 181, 181, 181, 181, 181, 181, 47, 36, 19, 19, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 181, 181, 181, 181, 47, 47, 19, 19, 19, 6, 1, 19, 181] 181
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 280
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078550 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078550
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078550/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078550/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078550
Building REAL300000078551
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078551'
/scratch/stefan/7769659/working/building/REAL300000078551 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078551

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078551/0 /scratch/stefan/7769659/working/building/REAL300000078551 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/489
`/scratch/stefan/7769659/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078551 none O=C([O-])COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 119, 65, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 119, 119, 29, 29, 29, 6, 1, 1, 29] 119
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 344
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078551 none O=C([O-])COC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [35, 21, 35, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 20, 29, 29, 29, 1, 21, 21, 1, 1, 1, 11, 29, 29, 1] 119
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28])
total number of confs: 190
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078551 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078551/1 /scratch/stefan/7769659/working/building/REAL300000078551 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/490
`/scratch/stefan/7769659/working/3D/490' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078551.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078551/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078551 none O=C([O-])COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 4, 4, 4, 4, 1, 4] 7
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 28])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078551 none O=C([O-])COC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 3, 3, 1, 1, 1, 3, 4, 1] 7
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27])
total number of confs: 12
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078551 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078551
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078551/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078551/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078551
Building REAL300000078552
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078552'
/scratch/stefan/7769659/working/building/REAL300000078552 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078552

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078552/0 /scratch/stefan/7769659/working/building/REAL300000078552 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/491
`/scratch/stefan/7769659/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)OC=C1)

`REAL300000078552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 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: [14, 12, 14, 12, 6, 2, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 15, 28, 28, 28, 1, 1, 12, 12, 12, 6, 6, 1, 1, 9, 28, 28, 1, 1, 12, 12] 64
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36])
total number of confs: 107
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 12, 12, 11, 11, 39, 39, 64, 64, 64, 60, 64, 64, 64, 12, 12, 1, 1, 1, 5, 5, 12, 12, 39, 64, 64, 12, 12, 1, 1] 64
rigid atoms, others: [1, 3, 4, 5, 35, 23, 24, 25, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 168
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 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, 41, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 64, 64, 64, 41, 41, 28, 28, 8, 1, 1, 28, 28, 64, 64] 64
rigid atoms, others: [32, 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, 33, 34, 35, 36])
total number of confs: 131
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078552 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078552/1 /scratch/stefan/7769659/working/building/REAL300000078552 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/492
`/scratch/stefan/7769659/working/3D/492' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)OC=C1)

`REAL300000078552.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078552/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 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: [13, 10, 13, 10, 6, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 14, 24, 24, 24, 1, 1, 10, 10, 10, 6, 6, 1, 1, 7, 24, 1, 1, 10, 10] 48
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 34, 35])
total number of confs: 94
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 9, 10, 10, 10, 10, 27, 27, 48, 48, 48, 47, 48, 48, 48, 10, 10, 1, 1, 1, 5, 5, 10, 10, 27, 48, 10, 10, 1, 1] 48
rigid atoms, others: [1, 34, 3, 4, 5, 35, 23, 24, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 120
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078552 none O=C([O-])C1=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 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, 30, 24, 24, 14, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 48, 48, 48, 30, 30, 24, 24, 7, 1, 24, 24, 48, 48] 48
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 122
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078552 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078552
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078552/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078552/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078552
Building REAL300000078553
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078553'
/scratch/stefan/7769659/working/building/REAL300000078553 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078553

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078553/0 /scratch/stefan/7769659/working/building/REAL300000078553 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/493
`/scratch/stefan/7769659/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NN2C(=O)C=NNC2=S)C(OCC(=O)[O-])=C1)

`REAL300000078553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078553 none COC1=CC=C(C=NN2C(=O)C=NNC2=S)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [35, 21, 8, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 75, 171, 179, 179, 21, 35, 35, 35, 21, 21, 7, 1, 1, 171, 171, 21] 179
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 604
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078553 none COC1=CC=C(C=NN2C(=O)C=NNC2=S)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 11, 21, 21, 21, 1, 1, 9, 48, 85, 85, 1, 3, 3, 3, 1, 1, 6, 21, 21, 48, 48, 1] 179
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 336
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078553 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078553/1 /scratch/stefan/7769659/working/building/REAL300000078553 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/494
`/scratch/stefan/7769659/working/3D/494' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(OCC(=O)[O-])=C1)

`REAL300000078553.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078553/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078553 none COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [23, 15, 7, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 46, 69, 74, 74, 15, 23, 23, 23, 15, 15, 7, 1, 69, 69, 15] 74
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078553 none COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 15, 15, 15, 1, 1, 8, 22, 36, 36, 1, 3, 3, 3, 1, 1, 5, 15, 22, 22, 1] 74
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078553 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078553
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078553/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078553/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078553
Building REAL300000078554
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078554'
/scratch/stefan/7769659/working/building/REAL300000078554 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078554

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078554/0 /scratch/stefan/7769659/working/building/REAL300000078554 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/495
`/scratch/stefan/7769659/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)

`REAL300000078554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078554 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 90, 197, 196, 21, 14, 47, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 9, 1, 1, 47, 47] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 678
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078554 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 31, 50, 7, 31, 31, 1, 1, 1, 1, 1, 1, 12, 12, 47, 47, 47, 25, 47, 47, 47, 1, 1, 1, 1, 12, 47, 47, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27])
total number of confs: 289
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078554 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078554/1 /scratch/stefan/7769659/working/building/REAL300000078554 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/496
`/scratch/stefan/7769659/working/3D/496' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)

`REAL300000078554.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078554/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078554 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 76, 136, 136, 29, 15, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 9, 1, 29, 29] 136
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 27, 28])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078554 none O=C([O-])C(F)(F)OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [44, 26, 44, 7, 26, 26, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 13, 29, 29, 29, 1, 1, 1, 1, 7, 29, 1, 1] 136
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078554 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078554
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078554/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078554/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078554
Building REAL300000078555
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078555'
/scratch/stefan/7769659/working/building/REAL300000078555 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078555

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078555/0 /scratch/stefan/7769659/working/building/REAL300000078555 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/497
`/scratch/stefan/7769659/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078555 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 5, 1, 1] 11
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078555 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 8, 11, 11] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078555 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078555/1 /scratch/stefan/7769659/working/building/REAL300000078555 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/498
`/scratch/stefan/7769659/working/3D/498' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078555.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078555/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078555 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 6, 1] 11
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078555 none CN1C(C(=O)[O-])=CC(Br)=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 2, 2, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 10, 11, 11, 11, 2, 2, 2, 1, 7, 11] 11
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078555 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078555
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078555/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078555/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078555
Building REAL300000078556
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078556'
/scratch/stefan/7769659/working/building/REAL300000078556 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078556

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078556/0 /scratch/stefan/7769659/working/building/REAL300000078556 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/499
`/scratch/stefan/7769659/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Br)

`REAL300000078556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078556 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 136, 27, 12, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 201, 201, 39, 39, 7, 1, 1, 39] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 573
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078556 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 44, 74, 10, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 21, 39, 39, 39, 1, 1, 1, 44, 44, 1, 1, 12, 39, 39, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28])
total number of confs: 345
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078556 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078556/1 /scratch/stefan/7769659/working/building/REAL300000078556 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/500
`/scratch/stefan/7769659/working/3D/500' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Br)

`REAL300000078556.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078556/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078556 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 99, 19, 16, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 182, 182, 44, 44, 8, 1, 44] 182
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28])
total number of confs: 598
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078556 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [69, 42, 69, 9, 1, 1, 1, 1, 1, 1, 13, 13, 44, 44, 44, 28, 44, 44, 44, 1, 1, 1, 42, 42, 1, 1, 13, 44, 1] 182
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27])
total number of confs: 327
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078556 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078556
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078556/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078556/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078556
Building REAL300000078557
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078557'
/scratch/stefan/7769659/working/building/REAL300000078557 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078557

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078557/0 /scratch/stefan/7769659/working/building/REAL300000078557 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/501
`/scratch/stefan/7769659/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=NNC2=S)C=C1)

`REAL300000078557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078557 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 7, 1, 1, 21, 21] 21
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078557 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 21, 21, 21, 16, 21, 21, 21, 1, 1, 3, 3, 3, 1, 11, 21, 21, 1, 1] 21
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 22, 23, 27, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 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
/scratch/stefan/7769659/working/building/REAL300000078557 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078557/1 /scratch/stefan/7769659/working/building/REAL300000078557 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/502
`/scratch/stefan/7769659/working/3D/502' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)

`REAL300000078557.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078557/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078557 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 11, 11] 11
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078557 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 11, 11, 11, 8, 11, 11, 11, 1, 1, 4, 4, 4, 1, 5, 11, 1, 1] 11
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 22, 23, 27, 30, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078557 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078557
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078557/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078557/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078557
Building REAL300000078558
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078558'
/scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000078558

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078558/0 /scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/503
`/scratch/stefan/7769659/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=NNC3=S)=C2C=C1)

`REAL300000078558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=NNC3=S)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 6, 1, 1, 9, 9] 9
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=NNC3=S)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 9, 9, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078558/1 /scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/504
`/scratch/stefan/7769659/working/3D/504' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=N[N-]C3=S)=C2C=C1)

`REAL300000078558.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078558/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=N[N-]C3=S)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 6, 6] 6
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 26, 27])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC2=NNC(C=NN3C(=O)C=N[N-]C3=S)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 4, 4, 6, 6, 6, 5, 6, 6, 6, 1, 1, 1, 1, 1, 4, 6, 1, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25])
total number of confs: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `2'
/scratch/stefan/7769659/working/building/REAL300000078558/2 /scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 2 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/505
`/scratch/stefan/7769659/working/3D/505' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NN3C(=O)C=NNC3=S)=NNC2=C1)

`REAL300000078558.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000078558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078558/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC=C2C(C=NN3C(=O)C=NNC3=S)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 8, 1, 1, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 11, 11] 11
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 27, 28])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078558 none O=C([O-])C1=CC=C2C(C=NN3C(=O)C=NNC3=S)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 8, 1, 1, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 4, 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, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078558 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078558
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078558/0.*
2: /scratch/stefan/7769659/working/building/REAL300000078558/2.*
1: /scratch/stefan/7769659/working/building/REAL300000078558/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078558
Building REAL300000078559
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078559'
/scratch/stefan/7769659/working/building/REAL300000078559 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078559

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078559/0 /scratch/stefan/7769659/working/building/REAL300000078559 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/506
`/scratch/stefan/7769659/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=NNC2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000078559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078559 none COC1=CC(C=NN2C(=O)C=NNC2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 100, 199, 201, 201, 45, 45, 45, 22, 7, 1, 1, 22, 199, 199] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35])
total number of confs: 607
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078559 none COC1=CC(C=NN2C(=O)C=NNC2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 13, 22, 22, 22, 1, 1, 2, 2, 1, 1, 1, 9, 55, 82, 82, 4, 4, 4, 1, 7, 22, 22, 1, 55, 55] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35])
total number of confs: 349
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078559 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078559/1 /scratch/stefan/7769659/working/building/REAL300000078559 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/507
`/scratch/stefan/7769659/working/3D/507' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000078559.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078559/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078559 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 118, 199, 201, 201, 59, 59, 59, 27, 9, 1, 27, 199, 199] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34])
total number of confs: 590
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078559 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 9, 27, 27, 27, 1, 1, 2, 2, 1, 1, 1, 9, 51, 82, 82, 4, 4, 4, 1, 6, 27, 1, 51, 51] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 33, 34])
total number of confs: 353
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078559 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078559
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078559/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078559/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078559
Building REAL300000078560
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078560'
/scratch/stefan/7769659/working/building/REAL300000078560 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078560

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078560/0 /scratch/stefan/7769659/working/building/REAL300000078560 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/508
`/scratch/stefan/7769659/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078560 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [10, 8, 10, 14, 14, 14, 8, 8, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 14, 8, 8, 8, 5, 1, 1] 14
rigid atoms, others: [35, 36, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078560 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [3, 1, 3, 7, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 8, 8, 8, 7, 8, 8, 8, 3, 3, 3, 7, 7, 1, 1, 1, 4, 8, 8] 14
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078560 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078560/1 /scratch/stefan/7769659/working/building/REAL300000078560 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/509
`/scratch/stefan/7769659/working/3D/509' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078560.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078560/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078560 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 3
rigid atoms, others: [35, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 4
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078560 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 1, 1, 1, 3, 3] 3
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078560 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078560
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078560/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078560/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078560
Building REAL300000078561
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078561'
/scratch/stefan/7769659/working/building/REAL300000078561 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078561

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078561/0 /scratch/stefan/7769659/working/building/REAL300000078561 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/510
`/scratch/stefan/7769659/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCCC(=O)[O-])

`REAL300000078561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078561 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 28, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 113, 182, 196, 201, 196, 56, 56, 56, 28, 7, 1, 1, 28, 28, 182, 182, 196, 196] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 615
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078561 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 12, 28, 28, 28, 1, 1, 1, 1, 9, 37, 51, 82, 77, 3, 3, 3, 1, 6, 28, 28, 1, 1, 37, 37, 51, 51] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 27, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078561 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078561/1 /scratch/stefan/7769659/working/building/REAL300000078561 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/511
`/scratch/stefan/7769659/working/3D/511' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCCC(=O)[O-])

`REAL300000078561.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078561/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078561 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 118, 183, 196, 201, 198, 65, 65, 65, 33, 9, 1, 33, 33, 183, 183, 196, 196] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 635
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078561 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 12, 33, 33, 33, 1, 1, 1, 1, 9, 38, 50, 84, 78, 3, 3, 3, 1, 7, 33, 1, 1, 38, 38, 50, 50] 201
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 27, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 32, 33, 34, 35])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078561 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078561
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078561/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078561/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078561
Building REAL300000078562
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078562'
/scratch/stefan/7769659/working/building/REAL300000078562 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078562

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078562/0 /scratch/stefan/7769659/working/building/REAL300000078562 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/512
`/scratch/stefan/7769659/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NN2C(=O)C=NNC2=S)C(Cl)=C1)

`REAL300000078562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078562 none O=C([O-])C1=CC=C(C=NN2C(=O)C=NNC2=S)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 6, 1, 1, 11] 11
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078562 none O=C([O-])C1=CC=C(C=NN2C(=O)C=NNC2=S)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 11, 1] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078562 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078562/1 /scratch/stefan/7769659/working/building/REAL300000078562 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/513
`/scratch/stefan/7769659/working/3D/513' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(Cl)=C1)

`REAL300000078562.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078562/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078562 none O=C([O-])C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 6, 1, 8] 8
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 24])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078562 none O=C([O-])C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 1] 8
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078562 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078562
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078562/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078562/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078562
Building REAL300000078563
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078563'
/scratch/stefan/7769659/working/building/REAL300000078563 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078563

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078563/0 /scratch/stefan/7769659/working/building/REAL300000078563 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/514
`/scratch/stefan/7769659/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)C(=O)[O-])

`REAL300000078563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078563 none CC(OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [111, 66, 13, 9, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 111, 115, 115, 111, 111, 111, 111, 39, 39, 9, 1, 1, 39, 39] 115
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 409
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078563 none CC(OC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 2, 2, 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: [25, 7, 1, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 22, 39, 39, 39, 1, 1, 25, 37, 37, 25, 25, 25, 25, 1, 1, 11, 39, 39, 1, 1] 116
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 17, 18, 26, 27, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30])
total number of confs: 219
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078563 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078563/1 /scratch/stefan/7769659/working/building/REAL300000078563 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/515
`/scratch/stefan/7769659/working/3D/515' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)C(=O)[O-])

`REAL300000078563.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078563/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078563 none CC(OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 53, 33, 16, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 75, 75, 75, 75, 75, 75, 75, 33, 33, 9, 1, 33, 33] 75
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 252
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078563 none CC(OC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 16, 33, 33, 33, 1, 1, 15, 23, 23, 15, 15, 15, 15, 1, 1, 9, 33, 1, 1] 75
rigid atoms, others: [2, 3, 4, 5, 6, 7, 17, 18, 26, 27, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 165
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078563 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078563
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078563/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078563/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078563
Building REAL300000078564
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078564'
/scratch/stefan/7769659/working/building/REAL300000078564 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078564

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078564/0 /scratch/stefan/7769659/working/building/REAL300000078564 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/516
`/scratch/stefan/7769659/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NN2C(=O)C=NNC2=S)C2=CC=CC=C21)

`REAL300000078564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078564 none O=C([O-])CN1C=C(C=NN2C(=O)C=NNC2=S)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', '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, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 30, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 77, 77, 30, 7, 1, 1, 30, 30, 30, 30] 77
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078564 none O=C([O-])CN1C=C(C=NN2C(=O)C=NNC2=S)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', '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, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 1, 1, 1, 1, 1, 12, 12, 30, 30, 30, 21, 30, 30, 30, 1, 1, 1, 1, 1, 1, 8, 8, 1, 12, 30, 30, 1, 1, 1, 1] 77
rigid atoms, others: [32, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078564 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078564/1 /scratch/stefan/7769659/working/building/REAL300000078564 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/517
`/scratch/stefan/7769659/working/3D/517' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NN2C(=O)C=N[N-]C2=S)C2=CC=CC=C21)

`REAL300000078564.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078564/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078564 none O=C([O-])CN1C=C(C=NN2C(=O)C=N[N-]C2=S)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 60, 60, 27, 8, 1, 27, 27, 27, 27] 60
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078564 none O=C([O-])CN1C=C(C=NN2C(=O)C=N[N-]C2=S)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 18, 27, 27, 27, 1, 1, 1, 1, 1, 1, 8, 8, 1, 9, 27, 1, 1, 1, 1] 60
rigid atoms, others: [3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 28, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078564 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078564
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078564/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078564/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078564
Building REAL300000078565
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078565'
/scratch/stefan/7769659/working/building/REAL300000078565 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078565

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078565/0 /scratch/stefan/7769659/working/building/REAL300000078565 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/518
`/scratch/stefan/7769659/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078565 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1] 13
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078565 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 2, 2, 1, 1, 1, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 2, 2, 2, 1, 11, 13, 13] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078565 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078565/1 /scratch/stefan/7769659/working/building/REAL300000078565 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/519
`/scratch/stefan/7769659/working/3D/519' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078565.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078565/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078565 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1] 15
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078565 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 2, 2, 1, 1, 1, 10, 10, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 2, 2, 2, 1, 10, 15] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078565 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078565
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078565/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078565/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078565
Building REAL300000078566
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078566'
/scratch/stefan/7769659/working/building/REAL300000078566 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078566

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078566/0 /scratch/stefan/7769659/working/building/REAL300000078566 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/520
`/scratch/stefan/7769659/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1Cl)

`REAL300000078566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078566 none O=C([O-])C1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1] 12
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078566 none O=C([O-])C1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 9, 12, 12, 12, 1, 1, 1, 1, 1, 6, 12, 12] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078566 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078566/1 /scratch/stefan/7769659/working/building/REAL300000078566 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/521
`/scratch/stefan/7769659/working/3D/521' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1Cl)

`REAL300000078566.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078566/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078566 none O=C([O-])C1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 6, 1] 11
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23])
total number of confs: 14
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078566 none O=C([O-])C1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 16, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 8, 11, 11, 11, 1, 1, 1, 1, 1, 5, 11] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078566 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078566
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078566/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078566/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078566
Building REAL300000078567
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078567'
/scratch/stefan/7769659/working/building/REAL300000078567 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078567

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078567/0 /scratch/stefan/7769659/working/building/REAL300000078567 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/522
`/scratch/stefan/7769659/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C1=CC=CC=C1)

`REAL300000078567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 201, 92, 18, 18, 18, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 191, 201, 201, 191, 201, 201, 191, 18, 18, 18, 6, 1, 1, 18, 201, 201, 191, 201, 201] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 678
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 34, 45, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 11, 18, 18, 18, 1, 34, 46, 46, 34, 46, 46, 34, 1, 1, 1, 7, 18, 18, 1, 46, 46, 34, 46, 46] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 263
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=NNC2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 3, 9, 46, 46, 46, 46, 46, 113, 113, 201, 201, 201, 181, 201, 201, 201, 46, 1, 1, 1, 1, 1, 1, 3, 46, 46, 46, 113, 201, 201, 46, 1, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 3, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 486
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078567 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078567/1 /scratch/stefan/7769659/working/building/REAL300000078567 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/523
`/scratch/stefan/7769659/working/3D/523' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C1=CC=CC=C1)

`REAL300000078567.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078567/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 201, 87, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 184, 201, 201, 184, 201, 201, 184, 22, 22, 22, 6, 1, 22, 201, 201, 184, 201, 201] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 711
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 51, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 13, 22, 22, 22, 1, 34, 46, 46, 34, 46, 46, 34, 1, 1, 1, 7, 22, 1, 46, 46, 34, 46, 46] 201
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 298
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078567 none O=C([O-])C(OC1=CC=CC(C=NN2C(=O)C=N[N-]C2=S)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 5, 1, 4, 11, 46, 46, 46, 46, 46, 104, 104, 201, 201, 201, 177, 201, 201, 201, 46, 1, 1, 1, 1, 1, 1, 4, 46, 46, 46, 104, 201, 46, 1, 1, 1, 1, 1] 201
rigid atoms, others: [34, 3, 36, 37, 38, 35, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 487
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078567 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078567
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078567/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078567/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078567
Building REAL300000078568
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078568'
/scratch/stefan/7769659/working/building/REAL300000078568 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078568

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078568/0 /scratch/stefan/7769659/working/building/REAL300000078568 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/524
`/scratch/stefan/7769659/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)C=C1)

`REAL300000078568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 6, 9, 9, 9, 1, 1, 3, 3, 3, 3, 1, 1, 3, 9, 9, 1, 1, 3, 3] 11
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 34, 35])
total number of confs: 36
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 11, 11, 11, 9, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 11, 3, 3, 1, 1] 11
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: 32
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 11, 9, 11, 11, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 9, 9, 9, 1, 1, 9, 9, 11, 11] 11
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, 34, 35])
total number of confs: 28
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078568 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078568/1 /scratch/stefan/7769659/working/building/REAL300000078568 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/525
`/scratch/stefan/7769659/working/3D/525' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)C=C1)

`REAL300000078568.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078568/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 9, 12, 12, 12, 1, 1, 3, 3, 3, 3, 1, 1, 6, 12, 1, 1, 3, 3] 13
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 33, 34])
total number of confs: 42
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 3, 1, 1, 8, 8, 13, 13, 13, 11, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 8, 13, 3, 3, 1, 1] 13
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078568 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 11, 13, 11, 13, 13, 11, 9, 11, 11, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 13, 13, 13, 13, 11, 11, 9, 1, 11, 11, 13, 13] 13
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 42
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078568 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078568
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078568/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078568/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078568
Building REAL300000078569
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078569'
/scratch/stefan/7769659/working/building/REAL300000078569 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078569

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078569/0 /scratch/stefan/7769659/working/building/REAL300000078569 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/526
`/scratch/stefan/7769659/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=C1)

`REAL300000078569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078569 none O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.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, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 6, 1, 1, 8] 8
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 11
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078569 none O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.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, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 6, 8, 8, 8, 1, 1, 1, 1, 1, 1, 4, 8, 8, 1] 8
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28])
total number of confs: 20
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078569 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078569/1 /scratch/stefan/7769659/working/building/REAL300000078569 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/527
`/scratch/stefan/7769659/working/3D/527' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1)

`REAL300000078569.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078569/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078569 none O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 6] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 28])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078569 none O=C([O-])C1=CC=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27])
total number of confs: 12
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078569 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078569
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078569/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078569/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078569
Building REAL300000078570
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078570'
/scratch/stefan/7769659/working/building/REAL300000078570 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078570

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078570/0 /scratch/stefan/7769659/working/building/REAL300000078570 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/528
`/scratch/stefan/7769659/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=NNC2=S)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000078570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078570 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [85, 41, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 107, 164, 164, 188, 188, 85, 85, 85, 41, 8, 1, 1, 41, 164, 164, 164, 164] 188
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 591
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078570 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 41, 41, 41, 24, 41, 41, 41, 1, 1, 1, 1, 1, 6, 17, 17, 27, 27, 3, 3, 3, 1, 13, 41, 41, 1, 17, 18, 18, 18] 188
rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 210
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078570 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078570/1 /scratch/stefan/7769659/working/building/REAL300000078570 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/529
`/scratch/stefan/7769659/working/3D/529' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000078570.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078570/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078570 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [90, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 102, 152, 152, 159, 159, 90, 90, 90, 43, 8, 1, 43, 152, 152, 152, 152] 159
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078570 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 43, 43, 43, 22, 43, 43, 43, 1, 1, 1, 1, 1, 6, 17, 17, 26, 26, 4, 4, 4, 1, 12, 43, 1, 17, 17, 17, 17] 159
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 28, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 32, 33, 34, 35])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078570 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078570
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078570/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078570/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078570
Building REAL300000078571
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078571'
/scratch/stefan/7769659/working/building/REAL300000078571 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078571

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078571/0 /scratch/stefan/7769659/working/building/REAL300000078571 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/530
`/scratch/stefan/7769659/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078571 none O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 6, 1, 1, 23] 23
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078571 none O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 16, 23, 23, 23, 1, 10, 23, 23, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078571 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078571/1 /scratch/stefan/7769659/working/building/REAL300000078571 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/531
`/scratch/stefan/7769659/working/3D/531' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078571.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078571/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078571 none O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 8, 1, 23] 23
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 21])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078571 none O=C([O-])C1=C(Cl)SC(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 14, 23, 23, 23, 1, 8, 23, 1] 23
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 21] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078571 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078571
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078571/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078571/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078571
Building REAL300000078572
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078572'
/scratch/stefan/7769659/working/building/REAL300000078572 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078572

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078572/0 /scratch/stefan/7769659/working/building/REAL300000078572 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/532
`/scratch/stefan/7769659/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078572 none O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 6, 1, 1] 11
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078572 none O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 8, 11, 11, 11, 1, 1, 5, 11, 11] 11
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078572 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078572/1 /scratch/stefan/7769659/working/building/REAL300000078572 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/533
`/scratch/stefan/7769659/working/3D/533' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078572.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078572/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078572 none O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 6, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 6, 1] 10
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078572 none O=C([O-])C1=CN=C(Cl)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 4, 10] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078572 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078572
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078572/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078572/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078572
Building REAL300000078573
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078573'
/scratch/stefan/7769659/working/building/REAL300000078573 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078573

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078573/0 /scratch/stefan/7769659/working/building/REAL300000078573 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/534
`/scratch/stefan/7769659/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)O2)=CC=C1O)

`REAL300000078573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 16, 26, 26, 26, 1, 13, 13, 12, 12, 13, 1, 1, 10, 26, 26, 13, 13, 26] 182
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 158
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 61, 61, 91, 91, 91, 87, 91, 91, 91, 13, 1, 1, 1, 1, 1, 13, 13, 61, 91, 91, 1, 1, 2] 182
rigid atoms, others: [32, 1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 33])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 91, 91, 91, 26, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 91, 91, 91, 91, 91, 26, 26, 7, 1, 1, 91, 91, 182] 182
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 295
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078573 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078573/1 /scratch/stefan/7769659/working/building/REAL300000078573 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/535
`/scratch/stefan/7769659/working/3D/535' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)O2)=CC=C1O)

`REAL300000078573.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078573/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 15, 27, 27, 27, 1, 13, 13, 12, 12, 13, 1, 1, 9, 27, 13, 13, 26] 144
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 45, 45, 72, 72, 72, 67, 72, 72, 72, 13, 1, 1, 1, 1, 1, 13, 13, 45, 72, 1, 1, 2] 144
rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 30, 31] set([0, 32, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078573 none O=C([O-])C1=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 72, 27, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 72, 72, 72, 72, 72, 27, 27, 8, 1, 72, 72, 144] 144
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32])
total number of confs: 238
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078573 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078573
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078573/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078573/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078573
Building REAL300000078574
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078574'
/scratch/stefan/7769659/working/building/REAL300000078574 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078574

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078574/0 /scratch/stefan/7769659/working/building/REAL300000078574 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/536
`/scratch/stefan/7769659/working/3D/536' -> `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=NN1C(=O)C=NNC1=S)

`REAL300000078574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078574 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1] 15
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 20
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078574 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 1, 1, 1, 11, 15, 15] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 49
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078574 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078574/1 /scratch/stefan/7769659/working/building/REAL300000078574 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/537
`/scratch/stefan/7769659/working/3D/537' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078574.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078574/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078574 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 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: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1] 15
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 20
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078574 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 1, 1, 1, 9, 15] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 32, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 51
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078574 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078574
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078574/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078574/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078574
Building REAL300000078575
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078575'
/scratch/stefan/7769659/working/building/REAL300000078575 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078575

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078575/0 /scratch/stefan/7769659/working/building/REAL300000078575 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/538
`/scratch/stefan/7769659/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)C=C1)

`REAL300000078575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 18, 13, 18, 18, 18, 1, 7, 7, 7, 7, 1, 1, 9, 18, 18, 7, 7] 32
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 10, 10, 10, 10, 25, 25, 32, 32, 32, 32, 32, 32, 32, 10, 1, 1, 1, 1, 10, 10, 25, 32, 32, 1, 1] 32
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.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, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 20, 32, 32, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 32, 18, 18, 6, 1, 1, 32, 32] 32
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 96
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078575 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078575/1 /scratch/stefan/7769659/working/building/REAL300000078575 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/539
`/scratch/stefan/7769659/working/3D/539' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)C=C1)

`REAL300000078575.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078575/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 13, 21, 21, 21, 1, 7, 7, 7, 7, 1, 1, 8, 21, 7, 7] 32
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 25, 32, 32, 32, 32, 32, 32, 32, 8, 1, 1, 1, 1, 8, 8, 25, 32, 1, 1] 32
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: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078575 none O=C([O-])C1=CC=C(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 21, 32, 32, 21, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 32, 32, 32, 32, 21, 21, 8, 1, 32, 32] 32
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 96
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078575 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078575
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078575/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078575/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078575
Building REAL300000078576
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078576'
/scratch/stefan/7769659/working/building/REAL300000078576 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078576

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078576/0 /scratch/stefan/7769659/working/building/REAL300000078576 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/540
`/scratch/stefan/7769659/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)=C1)

`REAL300000078576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 22, 29, 29, 29, 1, 13, 12, 13, 13, 1, 1, 12, 29, 29, 13] 68
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 68, 68, 68, 68, 68, 68, 68, 13, 1, 1, 1, 1, 13, 13, 50, 68, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 68, 68, 68, 68, 29, 29, 9, 1, 1, 68] 68
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 92
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078576 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078576/1 /scratch/stefan/7769659/working/building/REAL300000078576 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/541
`/scratch/stefan/7769659/working/3D/541' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)=C1)

`REAL300000078576.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078576/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 18, 35, 35, 35, 1, 13, 12, 13, 13, 1, 1, 11, 35, 13] 60
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 43, 43, 60, 60, 60, 60, 60, 60, 60, 13, 1, 1, 1, 1, 13, 13, 43, 60, 1] 60
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078576 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 35, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 60, 60, 60, 60, 35, 35, 8, 1, 60] 60
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 80
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078576 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078576
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078576/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078576/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078576
Building REAL300000078577
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078577'
/scratch/stefan/7769659/working/building/REAL300000078577 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078577

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078577/0 /scratch/stefan/7769659/working/building/REAL300000078577 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/542
`/scratch/stefan/7769659/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=NNC2=S)S1)

`REAL300000078577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078577 none CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=NNC2=S)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 11, 11, 11, 11, 11, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 26, 11, 6, 1, 1] 26
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078577 none CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=NNC2=S)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 3, 3, 1, 1, 3, 3, 11, 11, 11, 4, 11, 11, 11, 1, 5, 5, 5, 4, 4, 1, 3, 11, 11] 26
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078577 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078577/1 /scratch/stefan/7769659/working/building/REAL300000078577 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/543
`/scratch/stefan/7769659/working/3D/543' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=N[N-]C2=S)S1)

`REAL300000078577.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078577/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078577 none CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=N[N-]C2=S)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 13, 13, 13, 13, 13, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 27, 27, 27, 27, 27, 13, 7, 1] 27
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078577 none CCC1=CC(C(=O)[O-])=C(C=NN2C(=O)C=N[N-]C2=S)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 6, 13, 13, 13, 1, 8, 8, 8, 8, 8, 1, 3, 13] 27
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 19, 25] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078577 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078577
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078577/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078577/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078577
Building REAL300000078578
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078578'
/scratch/stefan/7769659/working/building/REAL300000078578 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078578

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078578/0 /scratch/stefan/7769659/working/building/REAL300000078578 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/544
`/scratch/stefan/7769659/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078578 none COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 6, 1, 1] 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])
total number of confs: 28
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078578 none COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 1, 1, 1, 1, 1, 12, 12, 24, 24, 24, 22, 24, 24, 24, 4, 4, 4, 1, 1, 1, 12, 24, 24] 24
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078578 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078578/1 /scratch/stefan/7769659/working/building/REAL300000078578 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/545
`/scratch/stefan/7769659/working/3D/545' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078578.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078578/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078578 none COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 7, 1] 27
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078578 none COC1=CC=C(C(=O)[O-])C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 19, 27, 27, 27, 4, 4, 4, 1, 1, 1, 11, 27] 27
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078578 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078578
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078578/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078578/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078578
Building REAL300000078579
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078579'
/scratch/stefan/7769659/working/building/REAL300000078579 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078579

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078579/0 /scratch/stefan/7769659/working/building/REAL300000078579 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/546
`/scratch/stefan/7769659/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=NNC3=S)C2=C1)

`REAL300000078579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078579 none O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=NNC3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 1, 1, 7] 7
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 9
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078579 none O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=NNC3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 1] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078579 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078579/1 /scratch/stefan/7769659/working/building/REAL300000078579 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/547
`/scratch/stefan/7769659/working/3D/547' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1)

`REAL300000078579.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078579/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078579 none O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 6] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 27])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078579 none O=C([O-])C1=CC=C2SC=C(C=NN3C(=O)C=N[N-]C3=S)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 6, 1] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078579 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078579
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078579/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078579/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078579
Building REAL300000078580
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078580'
/scratch/stefan/7769659/working/building/REAL300000078580 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078580

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078580/0 /scratch/stefan/7769659/working/building/REAL300000078580 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/548
`/scratch/stefan/7769659/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078580 none O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 6, 1, 1, 12] 12
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078580 none O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 8, 12, 12, 1] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078580 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078580/1 /scratch/stefan/7769659/working/building/REAL300000078580 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/549
`/scratch/stefan/7769659/working/3D/549' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078580.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078580/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078580 none O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 6, 1, 12] 12
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 24])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078580 none O=C([O-])C1=CC=C(Br)C(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 11, 12, 12, 12, 1, 1, 1, 8, 12, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23])
total number of confs: 32
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078580 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078580
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078580/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078580/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078580
Building REAL300000078581
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078581'
/scratch/stefan/7769659/working/building/REAL300000078581 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078581

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078581/0 /scratch/stefan/7769659/working/building/REAL300000078581 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/550
`/scratch/stefan/7769659/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1C(=O)[O-])

`REAL300000078581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078581 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 39, 39, 39, 39, 39, 35, 9, 1, 1, 35, 35] 39
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078581 none COC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 2, 2, 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, 11, 11, 35, 35, 35, 19, 35, 35, 35, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 11, 35, 35, 1, 1] 39
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078581 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078581/1 /scratch/stefan/7769659/working/building/REAL300000078581 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/551
`/scratch/stefan/7769659/working/3D/551' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1C(=O)[O-])

`REAL300000078581.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078581/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078581 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 40, 40, 40, 40, 40, 35, 8, 1, 35, 35] 40
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078581 none COC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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, 11, 11, 35, 35, 35, 20, 35, 35, 35, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 11, 35, 1, 1] 40
rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078581 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078581
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078581/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078581/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078581
Building REAL300000078582
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078582'
/scratch/stefan/7769659/working/building/REAL300000078582 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078582

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078582/0 /scratch/stefan/7769659/working/building/REAL300000078582 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/552
`/scratch/stefan/7769659/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=NNC2=S)C(F)=C1)

`REAL300000078582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078582 none O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=NNC2=S)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 7, 5, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 5, 1, 1, 7] 7
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 25])
total number of confs: 24
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078582 none O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=NNC2=S)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 7, 7, 1] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078582 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078582/1 /scratch/stefan/7769659/working/building/REAL300000078582 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/553
`/scratch/stefan/7769659/working/3D/553' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=N[N-]C2=S)C(F)=C1)

`REAL300000078582.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078582/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078582 none O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=N[N-]C2=S)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 1, 7] 7
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 24])
total number of confs: 9
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078582 none O=C([O-])C1=CC(F)=C(C=NN2C(=O)C=N[N-]C2=S)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 7, 1] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078582 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078582
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078582/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078582/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078582
Building REAL300000078583
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078583'
/scratch/stefan/7769659/working/building/REAL300000078583 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000078583 as failed and skipping
/scratch/stefan/7769659/working /scratch/stefan/7769659
`/scratch/stefan/7769659/working/building/REAL300000078583' -> `/scratch/stefan/7769659/failed/REAL300000078583'
Building REAL300000078584
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078584'
/scratch/stefan/7769659/working/building/REAL300000078584 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078584

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078584/0 /scratch/stefan/7769659/working/building/REAL300000078584 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/554
`/scratch/stefan/7769659/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)O1)

`REAL300000078584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [51, 50, 51, 50, 50, 50, 13, 2, 1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 18, 31, 31, 31, 1, 1, 50, 50, 50, 13, 13, 1, 1, 10, 31, 31, 1, 1] 173
rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34])
total number of confs: 169
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 41, 50, 50, 50, 50, 112, 112, 173, 173, 173, 173, 173, 173, 173, 50, 50, 1, 1, 1, 8, 8, 50, 50, 112, 173, 173, 50, 50] 173
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 391
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [173, 173, 173, 173, 173, 173, 102, 37, 9, 9, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 173, 173, 173, 102, 102, 31, 31, 9, 1, 1, 31, 31] 173
rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 491
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078584 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078584/1 /scratch/stefan/7769659/working/building/REAL300000078584 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/555
`/scratch/stefan/7769659/working/3D/555' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)O1)

`REAL300000078584.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078584/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 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: [27, 26, 27, 26, 26, 26, 9, 2, 1, 1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 22, 37, 37, 37, 1, 1, 26, 26, 26, 9, 9, 1, 1, 12, 37, 1, 1] 104
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 145
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 22, 26, 26, 22, 26, 71, 71, 104, 104, 104, 104, 104, 104, 104, 26, 26, 1, 1, 1, 8, 8, 26, 26, 71, 104, 26, 26] 104
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 260
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078584 none O=C([O-])C1=CC=C(COC2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 75, 41, 37, 18, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 104, 104, 104, 75, 75, 37, 37, 9, 1, 37, 37] 104
rigid atoms, others: [33, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 337
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078584 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078584
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078584/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078584/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078584
Building REAL300000078585
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078585'
/scratch/stefan/7769659/working/building/REAL300000078585 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078585

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078585/0 /scratch/stefan/7769659/working/building/REAL300000078585 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/556
`/scratch/stefan/7769659/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=NNC2=S)=C1O)

`REAL300000078585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078585 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=NNC2=S)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 4, 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, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 44] 44
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078585 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=NNC2=S)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 22, 22, 17, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 2] 44
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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
/scratch/stefan/7769659/working/building/REAL300000078585 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078585/1 /scratch/stefan/7769659/working/building/REAL300000078585 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/557
`/scratch/stefan/7769659/working/3D/557' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1O)

`REAL300000078585.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078585/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078585 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 4, 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, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 8, 1, 38] 38
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078585 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 12, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 7, 19, 2] 38
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 58
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078585 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078585
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078585/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078585/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078585
Building REAL300000078586
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078586'
/scratch/stefan/7769659/working/building/REAL300000078586 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078586

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078586/0 /scratch/stefan/7769659/working/building/REAL300000078586 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/558
`/scratch/stefan/7769659/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1)

`REAL300000078586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [12, 5, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 17, 19, 19, 19, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 19, 19, 1, 1, 3] 46
rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 16, 16, 26, 26, 26, 24, 26, 26, 26, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 16, 26, 26, 3, 3, 1] 46
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 38, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=NNC3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 26, 26, 26, 26, 26, 15, 9, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 26, 46, 46, 26, 26, 26, 19, 19, 9, 1, 1, 19, 19, 26] 46
rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 197
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078586 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078586/1 /scratch/stefan/7769659/working/building/REAL300000078586 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/559
`/scratch/stefan/7769659/working/3D/559' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1)

`REAL300000078586.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078586/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 18, 18, 18, 15, 18, 18, 18, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 18, 1, 1, 3] 47
rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 37])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 15, 25, 25, 25, 22, 25, 25, 25, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 25, 3, 3, 1] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 28, 29, 30, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078586 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NN3C(=O)C=N[N-]C3=S)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 25, 25, 22, 25, 25, 17, 16, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 25, 47, 47, 25, 25, 25, 18, 18, 9, 1, 18, 18, 25] 47
rigid atoms, others: [34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37])
total number of confs: 192
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078586 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078586
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078586/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078586/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078586
Building REAL300000078587
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078587'
/scratch/stefan/7769659/working/building/REAL300000078587 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078587

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078587/0 /scratch/stefan/7769659/working/building/REAL300000078587 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/560
`/scratch/stefan/7769659/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Cl)=C1)

`REAL300000078587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078587 none O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 16, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 6, 1, 1, 10] 10
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 22])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078587 none O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 16, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 3, 3, 10, 10, 10, 6, 10, 10, 10, 1, 1, 1, 1, 3, 10, 10, 1] 10
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078587 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078587/1 /scratch/stefan/7769659/working/building/REAL300000078587 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/561
`/scratch/stefan/7769659/working/3D/561' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Cl)=C1)

`REAL300000078587.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078587/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078587 none O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 16, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 6, 1, 10] 10
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 21])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078587 none O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 16, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 3, 3, 10, 10, 10, 6, 10, 10, 10, 1, 1, 1, 1, 3, 10, 1] 10
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 21] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078587 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078587
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078587/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078587/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078587
Building REAL300000078588
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078588'
/scratch/stefan/7769659/working/building/REAL300000078588 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078588

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078588/0 /scratch/stefan/7769659/working/building/REAL300000078588 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/562
`/scratch/stefan/7769659/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-])

`REAL300000078588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078588 none CCOC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 56, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 81, 178, 190, 190, 88, 88, 88, 88, 88, 17, 4, 1, 1, 17, 17, 178, 178] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 802
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078588 none CCOC1=CC(C=NN2C(=O)C=NNC2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 12, 17, 17, 17, 1, 1, 1, 1, 9, 38, 64, 64, 27, 27, 27, 27, 27, 1, 6, 17, 17, 1, 1, 38, 38] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 34, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078588 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078588/1 /scratch/stefan/7769659/working/building/REAL300000078588 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/563
`/scratch/stefan/7769659/working/3D/563' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-])

`REAL300000078588.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078588/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078588 none CCOC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 71, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 82, 153, 172, 172, 102, 102, 102, 102, 102, 17, 5, 1, 17, 17, 153, 153] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 729
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078588 none CCOC1=CC(C=NN2C(=O)C=N[N-]C2=S)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 10, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 13, 17, 17, 17, 1, 1, 1, 1, 9, 32, 69, 69, 30, 30, 30, 30, 30, 1, 7, 17, 1, 1, 32, 32] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 34, 35])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078588 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078588
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078588/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078588/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078588
Building REAL300000078589
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078589'
/scratch/stefan/7769659/working/building/REAL300000078589 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078589

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078589/0 /scratch/stefan/7769659/working/building/REAL300000078589 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/564
`/scratch/stefan/7769659/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 12, 14, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 42, 42, 42, 40, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 25, 42, 42] 42
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 34])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 4, 4, 9, 9, 9, 6, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 4, 9, 9] 42
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 42, 42, 42, 42, 42, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 9, 6, 1, 1] 42
rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 97
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078589 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078589/1 /scratch/stefan/7769659/working/building/REAL300000078589 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/565
`/scratch/stefan/7769659/working/3D/565' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078589.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078589/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [17, 13, 17, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 43, 43, 43, 40, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 43] 43
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34])
total number of confs: 113
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 12, 12, 12, 7, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 12] 43
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078589 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [15, 12, 15, 12, 12, 12, 12, 43, 43, 43, 43, 43, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 7, 1] 43
rigid atoms, others: [35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 103
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078589 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078589
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078589/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078589/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078589
Building REAL300000078590
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078590'
/scratch/stefan/7769659/working/building/REAL300000078590 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078590

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078590/0 /scratch/stefan/7769659/working/building/REAL300000078590 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/566
`/scratch/stefan/7769659/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-])

`REAL300000078590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078590 none COC1=CC=C(C)C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 15, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 8, 1, 1] 19
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078590 none COC1=CC=C(C)C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 15, 15, 15, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 5, 15, 15] 19
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078590 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078590/1 /scratch/stefan/7769659/working/building/REAL300000078590 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/567
`/scratch/stefan/7769659/working/3D/567' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-])

`REAL300000078590.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078590/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078590 none COC1=CC=C(C)C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 15, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 8, 1] 19
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078590 none COC1=CC=C(C)C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 10, 15, 15, 15, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 6, 15] 19
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 52
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078590 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078590
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078590/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078590/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078590
Building REAL300000078591
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078591'
/scratch/stefan/7769659/working/building/REAL300000078591 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078591

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078591/0 /scratch/stefan/7769659/working/building/REAL300000078591 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/568
`/scratch/stefan/7769659/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-])

`REAL300000078591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078591 none CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 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, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1] 10
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 14
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078591 none CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=NNC2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 2, 2, 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, 1, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 10, 10] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078591 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078591/1 /scratch/stefan/7769659/working/building/REAL300000078591 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/569
`/scratch/stefan/7769659/working/3D/569' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-])

`REAL300000078591.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078591/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078591 none CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1] 10
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078591 none CN1C2=CC=C(F)C=C2C(C=NN2C(=O)C=N[N-]C2=S)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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, 1, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 10] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078591 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078591
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078591/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078591/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078591
Building REAL300000078592
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078592'
/scratch/stefan/7769659/working/building/REAL300000078592 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078592

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078592/0 /scratch/stefan/7769659/working/building/REAL300000078592 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/570
`/scratch/stefan/7769659/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Br)=C1)

`REAL300000078592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078592 none O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 17, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 6, 1, 1, 10] 10
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 22])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078592 none O=C([O-])C1=C(C=NN2C(=O)C=NNC2=S)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 17, 1, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 3, 3, 10, 10, 10, 6, 10, 10, 10, 1, 1, 1, 1, 3, 10, 10, 1] 10
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078592 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078592/1 /scratch/stefan/7769659/working/building/REAL300000078592 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/571
`/scratch/stefan/7769659/working/3D/571' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Br)=C1)

`REAL300000078592.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078592/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078592 none O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 17, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 6, 1, 10] 10
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 21])
total number of confs: 15
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078592 none O=C([O-])C1=C(C=NN2C(=O)C=N[N-]C2=S)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 14, 1, 17, 1, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 3, 3, 10, 10, 10, 6, 10, 10, 10, 1, 1, 1, 1, 3, 10, 1] 10
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 21] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078592 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078592
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078592/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078592/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078592
Building REAL300000078593
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078593'
/scratch/stefan/7769659/working/building/REAL300000078593 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078593

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078593/0 /scratch/stefan/7769659/working/building/REAL300000078593 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/572
`/scratch/stefan/7769659/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=CC=C1)

`REAL300000078593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078593 none O=C([O-])C1=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 16, 16, 16] 16
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29])
total number of confs: 22
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078593 none O=C([O-])C1=C2NC=C(C=NN3C(=O)C=NNC3=S)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 11, 16, 16, 16, 1, 1, 1, 1, 1, 1, 6, 16, 16, 1, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078593 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078593/1 /scratch/stefan/7769659/working/building/REAL300000078593 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/573
`/scratch/stefan/7769659/working/3D/573' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=CC=C1)

`REAL300000078593.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078593/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078593 none O=C([O-])C1=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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: [15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 6, 1, 15, 15, 15] 15
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078593 none O=C([O-])C1=C2NC=C(C=NN3C(=O)C=N[N-]C3=S)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 12, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 15, 1, 1, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078593 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078593
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078593/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078593/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078593
Building REAL300000078594
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078594'
/scratch/stefan/7769659/working/building/REAL300000078594 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078594

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078594/0 /scratch/stefan/7769659/working/building/REAL300000078594 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/574
`/scratch/stefan/7769659/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NN3C(=O)C=NNC3=S)=CC=C2O1)

`REAL300000078594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078594 none O=C([O-])C1=CC2=CC(C=NN3C(=O)C=NNC3=S)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 6, 1, 1, 12, 12] 12
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 27, 28])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078594 none O=C([O-])C1=CC2=CC(C=NN3C(=O)C=NNC3=S)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078594 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078594/1 /scratch/stefan/7769659/working/building/REAL300000078594 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/575
`/scratch/stefan/7769659/working/3D/575' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NN3C(=O)C=N[N-]C3=S)=CC=C2O1)

`REAL300000078594.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078594/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078594 none O=C([O-])C1=CC2=CC(C=NN3C(=O)C=N[N-]C3=S)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 6, 1, 12, 12] 12
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 26, 27])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078594 none O=C([O-])C1=CC2=CC(C=NN3C(=O)C=N[N-]C3=S)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 11, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 12, 1, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078594 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078594
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078594/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078594/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078594
Building REAL300000078595
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078595'
/scratch/stefan/7769659/working/building/REAL300000078595 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078595

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078595/0 /scratch/stefan/7769659/working/building/REAL300000078595 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/576
`/scratch/stefan/7769659/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NN3C(=O)C=NNC3=S)=CC=CN12)

`REAL300000078595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078595 none O=C([O-])C1=CN=C2C(C=NN3C(=O)C=NNC3=S)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 1, 1, 7, 7, 7] 7
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 26, 27, 28])
total number of confs: 9
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078595 none O=C([O-])C1=CN=C2C(C=NN3C(=O)C=NNC3=S)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 4, 7, 7, 1, 1, 1] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078595 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078595/1 /scratch/stefan/7769659/working/building/REAL300000078595 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/577
`/scratch/stefan/7769659/working/3D/577' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NN3C(=O)C=N[N-]C3=S)=CC=CN12)

`REAL300000078595.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078595/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078595 none O=C([O-])C1=CN=C2C(C=NN3C(=O)C=N[N-]C3=S)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6] 6
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 25, 26, 27])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078595 none O=C([O-])C1=CN=C2C(C=NN3C(=O)C=N[N-]C3=S)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 5, 6, 6, 6, 1, 1, 1, 1, 1, 3, 6, 1, 1, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24])
total number of confs: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078595 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078595
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078595/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078595/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078595
Building REAL300000078596
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078596'
/scratch/stefan/7769659/working/building/REAL300000078596 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078596

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078596/0 /scratch/stefan/7769659/working/building/REAL300000078596 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/578
`/scratch/stefan/7769659/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=NNC2=S)O1)

`REAL300000078596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=NNC2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 7, 11, 11, 11, 118, 118, 118, 32, 32, 1, 1, 1, 1, 4, 11, 11] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 242
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=NNC2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 48, 118, 118, 101, 118, 118, 118, 141, 141, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 118, 118, 118, 118, 141, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=NNC2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 126, 40, 11, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 126, 126, 11, 11, 11, 11, 6, 1, 1] 201
rigid atoms, others: [35, 36, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 518
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078596 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078596/1 /scratch/stefan/7769659/working/building/REAL300000078596 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/579
`/scratch/stefan/7769659/working/3D/579' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=N[N-]C2=S)O1)

`REAL300000078596.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078596/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=N[N-]C2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 29, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 5, 17, 17, 17, 93, 93, 93, 29, 29, 1, 1, 1, 1, 5, 17] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=N[N-]C2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 50, 93, 93, 93, 93, 93, 93, 135, 135, 201, 201, 201, 172, 201, 201, 201, 1, 1, 1, 8, 8, 93, 93, 93, 93, 135, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078596 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NN2C(=O)C=N[N-]C2=S)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 70, 17, 17, 17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 145, 145, 17, 17, 17, 17, 9, 1] 201
rigid atoms, others: [35, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 552
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078596 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078596
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078596/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078596/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078596
Building REAL300000078597
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078597'
/scratch/stefan/7769659/working/building/REAL300000078597 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078597

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078597/0 /scratch/stefan/7769659/working/building/REAL300000078597 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/580
`/scratch/stefan/7769659/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078597 none O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078597 none O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 6, 6] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078597 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078597/1 /scratch/stefan/7769659/working/building/REAL300000078597 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/581
`/scratch/stefan/7769659/working/3D/581' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078597.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078597/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078597 none O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23])
total number of confs: 7
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078597 none O=C([O-])C1=C(Br)C=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 6] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078597 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078597
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078597/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078597/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078597
Building REAL300000078598
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078598'
/scratch/stefan/7769659/working/building/REAL300000078598 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078598

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078598/0 /scratch/stefan/7769659/working/building/REAL300000078598 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/582
`/scratch/stefan/7769659/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=NNC1=S)

`REAL300000078598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078598 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [16, 11, 11, 11, 11, 11, 15, 11, 11, 11, 11, 11, 11, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 15, 15, 15, 11, 11, 6, 1, 1] 17
rigid atoms, others: [36, 37, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078598 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 11, 11, 11, 8, 11, 11, 11, 3, 3, 3, 1, 3, 3, 3, 1, 1, 7, 11, 11] 17
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078598 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078598/1 /scratch/stefan/7769659/working/building/REAL300000078598 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/583
`/scratch/stefan/7769659/working/3D/583' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078598.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078598/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078598 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [18, 13, 13, 13, 13, 13, 17, 13, 13, 13, 13, 13, 13, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 17, 17, 17, 13, 13, 7, 1] 20
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078598 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 13, 13, 13, 9, 13, 13, 13, 2, 2, 2, 1, 3, 3, 3, 1, 1, 6, 13] 20
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 32, 35, 36, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078598 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078598
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078598/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078598/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078598
Building REAL300000078599
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078599'
/scratch/stefan/7769659/working/building/REAL300000078599 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078599

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078599/0 /scratch/stefan/7769659/working/building/REAL300000078599 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/584
`/scratch/stefan/7769659/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078599 none O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 6, 1, 1] 12
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078599 none O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 9, 12, 12, 12, 1, 1, 1, 1, 6, 12, 12] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078599 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078599/1 /scratch/stefan/7769659/working/building/REAL300000078599 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/585
`/scratch/stefan/7769659/working/3D/585' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078599.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078599/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078599 none O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 6, 1] 10
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078599 none O=C([O-])C1=CC=C2OCOC2=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 1, 1, 4, 10] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078599 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078599
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078599/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078599/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078599
Building REAL300000078600
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078600'
/scratch/stefan/7769659/working/building/REAL300000078600 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078600

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078600/0 /scratch/stefan/7769659/working/building/REAL300000078600 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/586
`/scratch/stefan/7769659/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=NNC2=S)=C1)

`REAL300000078600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078600 none N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 1, 1, 10] 10
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 26])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078600 none N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=NNC2=S)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 3, 3, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 1, 4, 10, 10, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 20, 21, 22, 26] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078600 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078600/1 /scratch/stefan/7769659/working/building/REAL300000078600 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/587
`/scratch/stefan/7769659/working/3D/587' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=N[N-]C2=S)=C1)

`REAL300000078600.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078600/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078600 none N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 1, 10] 10
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 25])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078600 none N#CC1=CC=C(C(=O)[O-])C(C=NN2C(=O)C=N[N-]C2=S)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 3, 3, 1, 1, 4, 4, 10, 10, 10, 7, 10, 10, 10, 1, 1, 1, 4, 10, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 20, 21, 22, 25] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078600 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078600
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078600/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078600/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078600
Building REAL300000078601
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078601'
/scratch/stefan/7769659/working/building/REAL300000078601 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078601

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078601/0 /scratch/stefan/7769659/working/building/REAL300000078601 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/588
`/scratch/stefan/7769659/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Cl)

`REAL300000078601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078601 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 126, 44, 21, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 201, 201, 44, 44, 8, 1, 1, 44] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 621
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078601 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 49, 78, 10, 1, 1, 1, 1, 1, 1, 12, 12, 44, 44, 44, 25, 44, 44, 44, 1, 1, 1, 49, 49, 1, 1, 12, 44, 44, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28])
total number of confs: 373
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078601 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078601/1 /scratch/stefan/7769659/working/building/REAL300000078601 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/589
`/scratch/stefan/7769659/working/3D/589' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Cl)

`REAL300000078601.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078601/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078601 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [186, 186, 186, 130, 45, 16, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 186, 186, 45, 45, 8, 1, 45] 186
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 28])
total number of confs: 549
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078601 none O=C([O-])COC1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [77, 41, 77, 9, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 45, 25, 45, 45, 45, 1, 1, 1, 41, 41, 1, 1, 13, 45, 1] 186
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27])
total number of confs: 361
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078601 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078601
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078601/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078601/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078601
Building REAL300000078602
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078602'
/scratch/stefan/7769659/working/building/REAL300000078602 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078602

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078602/0 /scratch/stefan/7769659/working/building/REAL300000078602 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/590
`/scratch/stefan/7769659/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1)

`REAL300000078602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078602 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 53, 25, 6, 25, 25, 6, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 54, 54, 53, 25, 25, 6, 1, 1, 25, 25] 54
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078602 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=NNC2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [14, 11, 14, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 15, 25, 25, 25, 1, 1, 11, 11, 5, 1, 1, 9, 25, 25, 1, 1] 54
rigid atoms, others: [32, 33, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078602 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078602/1 /scratch/stefan/7769659/working/building/REAL300000078602 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/591
`/scratch/stefan/7769659/working/3D/591' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1)

`REAL300000078602.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078602/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078602 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 52, 24, 6, 24, 24, 6, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 64, 64, 52, 24, 24, 6, 1, 24, 24] 64
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 290
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078602 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NN2C(=O)C=N[N-]C2=S)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [25, 16, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 14, 25, 25, 25, 1, 1, 16, 16, 5, 1, 1, 8, 25, 1, 1] 64
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 27, 28, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30])
total number of confs: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078602 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078602
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078602/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078602/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078602
Building REAL300000078603
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078603'
/scratch/stefan/7769659/working/building/REAL300000078603 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078603

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078603/0 /scratch/stefan/7769659/working/building/REAL300000078603 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/592
`/scratch/stefan/7769659/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NN3C(=O)C=NNC3=S)C(F)=CC=C2S1)

`REAL300000078603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078603 none O=C([O-])C1=CC2=C(C=NN3C(=O)C=NNC3=S)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 13, 13] 13
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078603 none O=C([O-])C1=CC2=C(C=NN3C(=O)C=NNC3=S)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 10, 10, 13, 13, 13, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 1, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26])
total number of confs: 34
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078603 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078603/1 /scratch/stefan/7769659/working/building/REAL300000078603 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/593
`/scratch/stefan/7769659/working/3D/593' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NN3C(=O)C=N[N-]C3=S)C(F)=CC=C2S1)

`REAL300000078603.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078603/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078603 none O=C([O-])C1=CC2=C(C=NN3C(=O)C=N[N-]C3=S)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 6, 1, 10, 10] 10
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27])
total number of confs: 14
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078603 none O=C([O-])C1=CC2=C(C=NN3C(=O)C=N[N-]C3=S)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 7, 7, 10, 10, 10, 9, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 10, 1, 1] 10
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078603 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078603
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078603/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078603/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078603
Building REAL300000078604
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078604'
/scratch/stefan/7769659/working/building/REAL300000078604 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078604

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078604/0 /scratch/stefan/7769659/working/building/REAL300000078604 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/594
`/scratch/stefan/7769659/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=NNC1=S)

`REAL300000078604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078604 none COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1] 16
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])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078604 none COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=NNC1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 16, 16, 16, 14, 16, 16, 16, 3, 3, 3, 1, 1, 1, 8, 16, 16] 16
rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 24, 25, 26] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078604 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078604/1 /scratch/stefan/7769659/working/building/REAL300000078604 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/595
`/scratch/stefan/7769659/working/3D/595' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=N[N-]C1=S)

`REAL300000078604.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078604/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078604 none COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 7, 1] 17
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078604 none COC1=CC(C(=O)[O-])=CC=C1C=NN1C(=O)C=N[N-]C1=S NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 1, 1, 1, 10, 17] 17
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078604 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078604
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078604/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078604/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078604
Building REAL300000078605
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078605'
/scratch/stefan/7769659/working/building/REAL300000078605 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078605

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078605/0 /scratch/stefan/7769659/working/building/REAL300000078605 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/596
`/scratch/stefan/7769659/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=NNC3=S)=N2)C1)

`REAL300000078605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=NNC3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [23, 13, 23, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 15, 27, 27, 27, 1, 13, 13, 13, 1, 1, 9, 27, 27, 13, 13] 84
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 139
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=NNC3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 52, 52, 84, 84, 84, 76, 84, 84, 84, 13, 1, 1, 1, 13, 13, 52, 84, 84, 1, 1] 84
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 199
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=NNC3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 3, 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, 27, 84, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 84, 84, 84, 27, 27, 8, 1, 1, 84, 84] 84
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 181
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078605 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078605/1 /scratch/stefan/7769659/working/building/REAL300000078605 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/597
`/scratch/stefan/7769659/working/3D/597' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=N[N-]C3=S)=N2)C1)

`REAL300000078605.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078605/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=N[N-]C3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [22, 13, 22, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 11, 20, 20, 20, 1, 13, 13, 13, 1, 1, 7, 20, 13, 13] 61
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 113
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=N[N-]C3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 34, 34, 61, 61, 61, 56, 61, 61, 61, 13, 1, 1, 1, 13, 13, 34, 61, 1, 1] 61
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29])
total number of confs: 141
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078605 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN3C(=O)C=N[N-]C3=S)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 11, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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, 61, 61, 20, 61, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 61, 61, 61, 20, 20, 9, 1, 61, 61] 61
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 136
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078605 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078605
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078605/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078605/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078605
Building REAL300000078606
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078606'
/scratch/stefan/7769659/working/building/REAL300000078606 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078606

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078606/0 /scratch/stefan/7769659/working/building/REAL300000078606 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/598
`/scratch/stefan/7769659/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=C(C)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1)

`REAL300000078606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078606 none CSCCON=C(C)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 21, 21, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 38, 38, 42, 52, 52, 1, 1, 29, 29, 29, 21, 21, 21, 21, 5, 5, 5, 1, 1, 17, 17, 17, 38, 38, 38, 38, 42, 42, 1, 1] 201
rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078606 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078606
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078606/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078606
Building REAL300000078607
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078607'
/scratch/stefan/7769659/working/building/REAL300000078607 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078607

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078607/0 /scratch/stefan/7769659/working/building/REAL300000078607 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/599
`/scratch/stefan/7769659/working/3D/599' -> `0.mol2'
Preparing input files

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

`REAL300000078607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078607 none CSCCON=C(C)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 114, 54, 34, 34, 2, 33, 2, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 201, 201, 201, 159, 159, 114, 114, 27, 34, 34, 11, 11, 1, 1, 11, 11] 201
rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078607 none CSCCON=C(C)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 53, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 123, 123, 123, 77, 77, 53, 53, 5, 5, 5, 1, 1, 11, 11, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 396
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078607 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078607
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078607/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078607
Building REAL300000078608
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078608'
/scratch/stefan/7769659/working/building/REAL300000078608 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078608

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078608/0 /scratch/stefan/7769659/working/building/REAL300000078608 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/600
`/scratch/stefan/7769659/working/3D/600' -> `0.mol2'
Preparing input files

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

`REAL300000078608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078608 none CSCCON=C(C)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 55, 49, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 27, 27, 1, 1, 91, 91, 91, 55, 55, 49, 49, 5, 5, 5, 1, 1, 9, 19, 19, 1, 1] 201
rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078608 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078608
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078608/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078608
Building REAL300000078609
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078609'
/scratch/stefan/7769659/working/building/REAL300000078609 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078609

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078609/0 /scratch/stefan/7769659/working/building/REAL300000078609 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/601
`/scratch/stefan/7769659/working/3D/601' -> `0.mol2'
Preparing input files

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

`REAL300000078609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078609 none CSCCON=C(C)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 36, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 18, 18, 28, 27, 1, 1, 55, 55, 55, 38, 38, 36, 36, 5, 5, 5, 1, 1, 5, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078609 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078609
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078609/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078609
Building REAL300000078610
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078610'
/scratch/stefan/7769659/working/building/REAL300000078610 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078610

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078610/0 /scratch/stefan/7769659/working/building/REAL300000078610 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/602
`/scratch/stefan/7769659/working/3D/602' -> `0.mol2'
Preparing input files

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

`REAL300000078610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078610 none CSCCON=C(C)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 39, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 21, 28, 30, 36, 36, 1, 1, 61, 61, 61, 41, 41, 39, 39, 5, 5, 5, 1, 1, 5, 21, 21, 28, 28, 30, 30, 1, 1] 201
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 44, 43, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078610 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078610
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078610/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078610
Building REAL300000078611
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078611'
/scratch/stefan/7769659/working/building/REAL300000078611 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078611

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078611/0 /scratch/stefan/7769659/working/building/REAL300000078611 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/603
`/scratch/stefan/7769659/working/3D/603' -> `0.mol2'
Preparing input files

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

`REAL300000078611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078611 none CSCCON=C(C)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 86, 58, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 14, 14, 1, 1, 134, 134, 134, 86, 86, 58, 58, 6, 6, 6, 1, 1, 5, 10, 10, 10, 1, 1] 201
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078611 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078611
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078611/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078611
Building REAL300000078612
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078612'
/scratch/stefan/7769659/working/building/REAL300000078612 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078612

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078612/0 /scratch/stefan/7769659/working/building/REAL300000078612 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/604
`/scratch/stefan/7769659/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078612 none CSCCON=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 36, 28, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 47, 47, 61, 61, 61, 36, 36, 28, 28, 4, 1, 1, 1, 27, 27] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078612 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078612
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078612/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078612
Building REAL300000078613
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078613'
/scratch/stefan/7769659/working/building/REAL300000078613 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078613

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078613/0 /scratch/stefan/7769659/working/building/REAL300000078613 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/605
`/scratch/stefan/7769659/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1)

`REAL300000078613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078613 none CSCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 146, 117, 43, 31, 31, 15, 15, 14, 15, 15, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 201, 201, 201, 146, 146, 117, 117, 31, 14, 15, 15, 5, 5, 1, 1, 1, 1, 15] 201
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 665
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078613 none CSCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 45, 35, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 7, 15, 15, 15, 15, 15, 15, 19, 19, 1, 74, 74, 74, 45, 45, 35, 35, 4, 1, 1, 1, 7, 7, 15, 15, 15, 15, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 41, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 262
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078613 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078613
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078613/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078613
Building REAL300000078614
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078614'
/scratch/stefan/7769659/working/building/REAL300000078614 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078614

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078614/0 /scratch/stefan/7769659/working/building/REAL300000078614 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/606
`/scratch/stefan/7769659/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1)

`REAL300000078614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078614 none CSCCON=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 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, 47, 35, 10, 5, 5, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 91, 91, 91, 46, 46, 35, 35, 5, 1, 1, 5, 5, 1] 120
rigid atoms, others: [33, 6, 7, 8, 9, 10, 11, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078614 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078614
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078614/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078614
Building REAL300000078615
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078615'
/scratch/stefan/7769659/working/building/REAL300000078615 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078615

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078615/0 /scratch/stefan/7769659/working/building/REAL300000078615 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/607
`/scratch/stefan/7769659/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1)

`REAL300000078615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078615 none CSCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 130, 96, 32, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 14, 14, 201, 201, 201, 130, 130, 96, 96, 14, 14, 14, 8, 8, 1, 2, 2, 2, 14, 14] 201
rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078615 none CSCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 26, 18, 4, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 14, 24, 24, 14, 1, 1, 58, 58, 58, 26, 26, 18, 18, 2, 1, 1, 2, 2, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078615 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078615
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078615/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078615
Building REAL300000078616
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078616'
/scratch/stefan/7769659/working/building/REAL300000078616 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078616

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078616/0 /scratch/stefan/7769659/working/building/REAL300000078616 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/608
`/scratch/stefan/7769659/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000078616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078616 none CSCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 152, 120, 45, 35, 35, 15, 15, 14, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 201, 201, 201, 152, 152, 120, 120, 35, 14, 15, 15, 7, 7, 1, 1, 1, 1, 15] 201
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 715
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078616 none CSCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 32, 22, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 54, 54, 54, 32, 32, 22, 22, 6, 1, 1, 1, 3, 3, 15, 15, 15, 15, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 41, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078616 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078616
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078616/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078616
Building REAL300000078617
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078617'
/scratch/stefan/7769659/working/building/REAL300000078617 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078617

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078617/0 /scratch/stefan/7769659/working/building/REAL300000078617 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/609
`/scratch/stefan/7769659/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1)

`REAL300000078617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078617 none CSCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 139, 97, 42, 26, 26, 19, 19, 19, 19, 10, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 201, 201, 201, 139, 139, 97, 97, 26, 19, 19, 6, 6, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 677
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078617 none CSCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 26, 20, 6, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 19, 19, 20, 20, 19, 19, 19, 1, 1, 63, 63, 63, 26, 26, 20, 20, 4, 1, 1, 10, 10, 19, 19, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 21, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 198
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078617 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078617
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078617/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078617
Building REAL300000078618
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078618'
/scratch/stefan/7769659/working/building/REAL300000078618 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078618

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078618/0 /scratch/stefan/7769659/working/building/REAL300000078618 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/610
`/scratch/stefan/7769659/working/3D/610' -> `0.mol2'
Preparing input files

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

`REAL300000078618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078618 none CSCCON=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 24, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 40, 40, 1, 1, 42, 42, 42, 23, 23, 18, 18, 1, 1, 1, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078618 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078618
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078618/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078618
Building REAL300000078619
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078619'
/scratch/stefan/7769659/working/building/REAL300000078619 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078619

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078619/0 /scratch/stefan/7769659/working/building/REAL300000078619 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/611
`/scratch/stefan/7769659/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=C(Br)C=C(C(=O)[O-])N1C)

`REAL300000078619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078619 none CSCCON=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 116, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 159, 159, 116, 116, 13, 1, 2, 2, 2] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28])
total number of confs: 687
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078619 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078619
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078619/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078619
Building REAL300000078620
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078620'
/scratch/stefan/7769659/working/building/REAL300000078620 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078620

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078620/0 /scratch/stefan/7769659/working/building/REAL300000078620 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/612
`/scratch/stefan/7769659/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCC(=O)[O-])C(Br)=C1)

`REAL300000078620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078620 none CSCCON=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 50, 37, 9, 4, 4, 1, 1, 1, 1, 1, 1, 7, 17, 26, 26, 1, 1, 1, 87, 87, 87, 49, 49, 38, 38, 4, 1, 1, 17, 17, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 18, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078620 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078620
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078620/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078620
Building REAL300000078621
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078621'
/scratch/stefan/7769659/working/building/REAL300000078621 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078621

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078621/0 /scratch/stefan/7769659/working/building/REAL300000078621 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/613
`/scratch/stefan/7769659/working/3D/613' -> `0.mol2'
Preparing input files

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

`REAL300000078621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078621 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NOCCSC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 27, 92, 137, 197, 1, 1, 4, 4, 4, 1, 8, 92, 92, 137, 137, 197, 197, 197, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 34, 19, 20, 24] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 664
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078621 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078621
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078621/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078621
Building REAL300000078622
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078622'
/scratch/stefan/7769659/working/building/REAL300000078622 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078622

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078622/0 /scratch/stefan/7769659/working/building/REAL300000078622 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/614
`/scratch/stefan/7769659/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1)

`REAL300000078622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078622 none CSCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 155, 63, 60, 60, 23, 22, 38, 38, 18, 10, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 201, 201, 201, 155, 155, 155, 155, 60, 38, 38, 10, 10, 6, 6, 1, 38] 201
rigid atoms, others: [39, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078622 none CSCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 19, 19, 4, 2, 2, 1, 1, 1, 1, 1, 1, 8, 15, 15, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 35, 35, 35, 19, 19, 19, 19, 2, 1, 1, 15, 15, 15, 15, 38, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 40, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078622 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078622
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078622/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078622
Building REAL300000078623
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078623'
/scratch/stefan/7769659/working/building/REAL300000078623 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078623

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078623/0 /scratch/stefan/7769659/working/building/REAL300000078623 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/615
`/scratch/stefan/7769659/working/3D/615' -> `0.mol2'
Preparing input files

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

`REAL300000078623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078623 none COC1=CC(C=NOCCSC)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 7, 25, 29, 66, 1, 1, 2, 2, 1, 1, 1, 9, 13, 21, 21, 3, 3, 3, 1, 3, 25, 25, 29, 29, 66, 66, 66, 1, 13, 13] 201
rigid atoms, others: [1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 35, 26] set([0, 6, 7, 8, 9, 10, 11, 14, 15, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078623 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078623
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078623/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078623
Building REAL300000078624
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078624'
/scratch/stefan/7769659/working/building/REAL300000078624 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078624

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078624/0 /scratch/stefan/7769659/working/building/REAL300000078624 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/616
`/scratch/stefan/7769659/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-])

`REAL300000078624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078624 none CSCCON=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [104, 48, 39, 12, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 19, 34, 34, 104, 104, 104, 48, 48, 39, 39, 4, 1, 1, 1, 4, 4, 4, 19, 19] 197
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 376
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078624 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078624
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078624/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078624
Building REAL300000078625
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078625'
/scratch/stefan/7769659/working/building/REAL300000078625 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078625

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078625/0 /scratch/stefan/7769659/working/building/REAL300000078625 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/617
`/scratch/stefan/7769659/working/3D/617' -> `0.mol2'
Preparing input files

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

`REAL300000078625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078625 none CSCCON=C(C)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 141, 110, 46, 30, 30, 10, 30, 5, 10, 10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 201, 201, 201, 141, 141, 110, 110, 30, 30, 30, 10, 10, 1, 1, 1, 1, 10, 10] 201
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: 673
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078625 none CSCCON=C(C)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 35, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 10, 10, 9, 9, 10, 10, 10, 10, 1, 1, 89, 89, 89, 47, 47, 35, 35, 5, 5, 5, 1, 1, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078625 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078625
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078625/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078625
Building REAL300000078626
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078626'
/scratch/stefan/7769659/working/building/REAL300000078626 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078626

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078626/0 /scratch/stefan/7769659/working/building/REAL300000078626 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/618
`/scratch/stefan/7769659/working/3D/618' -> `0.mol2'
Preparing input files

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

`REAL300000078626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078626 none COC1=CC(C=NOCCSC)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 7, 25, 29, 43, 1, 1, 1, 1, 7, 11, 11, 19, 17, 3, 3, 3, 1, 3, 25, 25, 29, 29, 43, 43, 43, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 34, 24] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078626 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078626
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078626/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078626
Building REAL300000078627
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078627'
/scratch/stefan/7769659/working/building/REAL300000078627 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078627

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078627/0 /scratch/stefan/7769659/working/building/REAL300000078627 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/619
`/scratch/stefan/7769659/working/3D/619' -> `0.mol2'
Preparing input files

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

`REAL300000078627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078627 none CSCCON=C(C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', '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, 12, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 11, 11, 17, 26, 26, 1, 33, 33, 33, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 11, 11, 11, 11, 17, 17, 1] 201
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 182
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078627 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078627
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078627/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078627
Building REAL300000078628
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078628'
/scratch/stefan/7769659/working/building/REAL300000078628 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078628

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078628/0 /scratch/stefan/7769659/working/building/REAL300000078628 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/620
`/scratch/stefan/7769659/working/3D/620' -> `0.mol2'
Preparing input files

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

`REAL300000078628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078628 none CSCCON=C(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', '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, 12, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 48, 17, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 20, 20, 1, 1, 83, 83, 83, 57, 57, 48, 48, 12, 12, 12, 3, 3, 1, 1, 1, 1, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 325
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078628 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078628
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078628/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078628
Building REAL300000078629
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078629'
/scratch/stefan/7769659/working/building/REAL300000078629 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078629

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078629/0 /scratch/stefan/7769659/working/building/REAL300000078629 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/621
`/scratch/stefan/7769659/working/3D/621' -> `0.mol2'
Preparing input files

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

`REAL300000078629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078629 none CSCCON=C(C)CCC1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', '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, 12, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 61, 53, 14, 12, 12, 4, 12, 2, 1, 1, 1, 1, 1, 1, 6, 14, 27, 27, 1, 1, 86, 86, 86, 61, 61, 53, 53, 12, 12, 12, 4, 4, 2, 2, 1, 1, 14, 14, 1, 1] 201
rigid atoms, others: [35, 36, 39, 40, 9, 10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078629 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078629
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078629/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078629
Building REAL300000078630
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078630'
/scratch/stefan/7769659/working/building/REAL300000078630 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078630

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078630/0 /scratch/stefan/7769659/working/building/REAL300000078630 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/622
`/scratch/stefan/7769659/working/3D/622' -> `0.mol2'
Preparing input files

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

`REAL300000078630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078630 none CSCCON=C(C)CCC1=CC=C(OCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', '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, 12, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 46, 42, 14, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 1, 1, 64, 64, 64, 46, 46, 42, 42, 12, 12, 12, 3, 3, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 43, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078630 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078630
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078630/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078630
Building REAL300000078631
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078631'
/scratch/stefan/7769659/working/building/REAL300000078631 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078631

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078631/0 /scratch/stefan/7769659/working/building/REAL300000078631 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/623
`/scratch/stefan/7769659/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000078631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078631 none CSCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 157, 122, 49, 49, 49, 20, 49, 10, 5, 5, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 201, 201, 201, 157, 157, 122, 122, 49, 49, 49, 20, 20, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50])
total number of confs: 811
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078631 none CSCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 39, 31, 11, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 11, 11, 10, 1, 1, 53, 53, 53, 39, 39, 31, 31, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 13, 14, 40, 50, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078631 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078631
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078631/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078631
Building REAL300000078632
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078632'
/scratch/stefan/7769659/working/building/REAL300000078632 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078632

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078632/0 /scratch/stefan/7769659/working/building/REAL300000078632 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/624
`/scratch/stefan/7769659/working/3D/624' -> `0.mol2'
Preparing input files

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

`REAL300000078632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078632 none CCC(=NOCCSC)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 5, 5, 14, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 6, 6, 7, 24, 24, 43, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 21, 21, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 24, 43, 43, 43, 1, 1, 7, 7, 14, 14, 15, 15, 15, 14, 1, 1] 201
rigid atoms, others: [2, 35, 36, 9, 10, 11, 12, 13, 46, 45, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078632 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078632
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078632/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078632
Building REAL300000078633
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078633'
/scratch/stefan/7769659/working/building/REAL300000078633 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078633

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078633/0 /scratch/stefan/7769659/working/building/REAL300000078633 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/625
`/scratch/stefan/7769659/working/3D/625' -> `0.mol2'
Preparing input files

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

`REAL300000078633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078633 none COC1=CC(C(C)=NOCCSC)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 12, 5, 5, 14, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 6, 10, 36, 38, 54, 1, 1, 1, 1, 5, 11, 13, 21, 28, 28, 3, 3, 3, 1, 7, 7, 7, 36, 36, 38, 38, 55, 55, 55, 1, 1, 11, 11, 13, 13, 21, 21] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 13, 14, 15, 16, 26, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078633 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078633
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078633/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078633
Building REAL300000078634
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078634'
/scratch/stefan/7769659/working/building/REAL300000078634 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078634

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078634/0 /scratch/stefan/7769659/working/building/REAL300000078634 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/626
`/scratch/stefan/7769659/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1)

`REAL300000078634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078634 none CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 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, 140, 96, 21, 5, 5, 5, 5, 1, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 140, 140, 96, 96, 5, 5, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [32, 8, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 695
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078634 none CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 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: [98, 54, 32, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 5, 1, 98, 98, 98, 54, 54, 32, 32, 1, 1, 5, 5, 4, 5, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 12, 19, 27, 28] set([0, 1, 2, 3, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078634 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078634
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078634/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078634
Building REAL300000078635
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078635'
/scratch/stefan/7769659/working/building/REAL300000078635 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078635

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078635/0 /scratch/stefan/7769659/working/building/REAL300000078635 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/627
`/scratch/stefan/7769659/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1)

`REAL300000078635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078635 none CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 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, 142, 97, 21, 5, 5, 5, 5, 1, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 142, 142, 97, 97, 5, 5, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [32, 8, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 706
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078635 none CSCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 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: [95, 52, 30, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 5, 1, 95, 95, 95, 52, 52, 30, 30, 1, 1, 5, 5, 3, 5, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 12, 19, 27, 28] set([0, 1, 2, 3, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078635 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078635
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078635/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078635
Building REAL300000078636
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078636'
/scratch/stefan/7769659/working/building/REAL300000078636 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078636

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078636/0 /scratch/stefan/7769659/working/building/REAL300000078636 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/628
`/scratch/stefan/7769659/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078636 none CSCCON=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 37, 33, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 45, 45, 78, 78, 78, 37, 37, 33, 33, 3, 3, 3, 1, 1, 1, 27, 27] 201
rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078636 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078636
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078636/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078636
Building REAL300000078637
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078637'
/scratch/stefan/7769659/working/building/REAL300000078637 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078637

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078637/0 /scratch/stefan/7769659/working/building/REAL300000078637 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/629
`/scratch/stefan/7769659/working/3D/629' -> `0.mol2'
Preparing input files

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

`REAL300000078637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078637 none CSCCON=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', '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, 12, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [193, 151, 123, 48, 9, 9, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 151, 151, 123, 123, 10, 10, 10, 2, 2, 1, 1, 2, 2, 2, 1] 201
rigid atoms, others: [34, 35, 6, 39, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 651
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078637 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078637
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078637/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078637
Building REAL300000078638
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078638'
/scratch/stefan/7769659/working/building/REAL300000078638 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078638

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078638/0 /scratch/stefan/7769659/working/building/REAL300000078638 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/630
`/scratch/stefan/7769659/working/3D/630' -> `0.mol2'
Preparing input files

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

`REAL300000078638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078638 none CSCCON=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 147, 54, 40, 40, 30, 30, 30, 30, 30, 8, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 30, 201, 201, 201, 159, 159, 147, 147, 40, 30, 30, 30, 3, 1, 1, 1, 1, 1, 30] 201
rigid atoms, others: [36, 37, 38, 39, 40, 13, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 659
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078638 none CSCCON=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 33, 27, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 26, 27, 27, 26, 30, 30, 26, 30, 30, 1, 63, 63, 63, 33, 33, 27, 27, 3, 1, 1, 1, 26, 30, 30, 26, 30, 30, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 41, 23] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 271
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078638 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078638
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078638/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078638
Building REAL300000078639
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078639'
/scratch/stefan/7769659/working/building/REAL300000078639 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078639

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078639/0 /scratch/stefan/7769659/working/building/REAL300000078639 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/631
`/scratch/stefan/7769659/working/3D/631' -> `0.mol2'
Preparing input files

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

`REAL300000078639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078639 none CSCCON=C(C)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [161, 80, 45, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 161, 161, 161, 80, 80, 45, 45, 3, 3, 3, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16] 201
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 513
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078639 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078639
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078639/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078639
Building REAL300000078640
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078640'
/scratch/stefan/7769659/working/building/REAL300000078640 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078640

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078640/0 /scratch/stefan/7769659/working/building/REAL300000078640 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/632
`/scratch/stefan/7769659/working/3D/632' -> `0.mol2'
Preparing input files

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

`REAL300000078640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078640 none CSCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 171, 130, 43, 9, 9, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 201, 201, 201, 171, 170, 128, 130, 9, 3, 3, 1, 1, 1, 1, 3, 3] 201
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: 708
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078640 none CSCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 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]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 128, 95, 26, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 160, 160, 160, 127, 127, 96, 96, 6, 1, 1, 3, 3, 3, 3, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 556
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078640 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078640
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078640/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078640
Building REAL300000078641
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078641'
/scratch/stefan/7769659/working/building/REAL300000078641 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078641

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078641/0 /scratch/stefan/7769659/working/building/REAL300000078641 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/633
`/scratch/stefan/7769659/working/3D/633' -> `0.mol2'
Preparing input files

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

`REAL300000078641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078641 none COC1=CC(C=NOCCSC)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 9, 35, 49, 87, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 4, 4, 4, 1, 5, 36, 36, 48, 48, 87, 86, 86, 1, 8, 8, 8, 8] 201
rigid atoms, others: [1, 2, 3, 4, 5, 16, 12, 13, 14, 15, 34, 25] set([0, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078641 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078641
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078641/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078641
Building REAL300000078642
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078642'
/scratch/stefan/7769659/working/building/REAL300000078642 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078642

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078642/0 /scratch/stefan/7769659/working/building/REAL300000078642 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/634
`/scratch/stefan/7769659/working/3D/634' -> `0.mol2'
Preparing input files

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

`REAL300000078642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078642 none CSCCON=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 163, 125, 52, 26, 26, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 163, 163, 125, 125, 26, 12, 12, 1, 1, 2, 1] 402
rigid atoms, others: [32, 33, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 691
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078642 none CSCCON=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [150, 82, 53, 13, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 12, 1, 150, 150, 150, 82, 82, 53, 53, 5, 1, 1, 12, 13, 24, 13] 402
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 488
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078642 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078642
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078642/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078642
Building REAL300000078643
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078643'
/scratch/stefan/7769659/working/building/REAL300000078643 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078643

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078643/0 /scratch/stefan/7769659/working/building/REAL300000078643 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/635
`/scratch/stefan/7769659/working/3D/635' -> `0.mol2'
Preparing input files

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

`REAL300000078643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078643 none CSCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 162, 119, 53, 28, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 162, 162, 119, 119, 28, 6, 6, 1, 1, 1, 1] 201
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: 712
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078643 none CSCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [156, 100, 65, 18, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 1, 156, 156, 156, 100, 100, 65, 65, 7, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 520
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078643 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078643
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078643/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078643
Building REAL300000078644
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078644'
/scratch/stefan/7769659/working/building/REAL300000078644 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078644

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078644/0 /scratch/stefan/7769659/working/building/REAL300000078644 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/636
`/scratch/stefan/7769659/working/3D/636' -> `0.mol2'
Preparing input files

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

`REAL300000078644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078644 none CSCCON=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 142, 108, 46, 30, 30, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 142, 142, 108, 108, 30, 12, 12, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 661
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078644 none CSCCON=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [119, 65, 45, 13, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 119, 119, 119, 65, 65, 45, 45, 4, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078644 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078644
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078644/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078644
Building REAL300000078645
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078645'
/scratch/stefan/7769659/working/building/REAL300000078645 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078645

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078645/0 /scratch/stefan/7769659/working/building/REAL300000078645 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/637
`/scratch/stefan/7769659/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(C(=O)[O-])=CC=C1Br)

`REAL300000078645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078645 none CSCCON=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', '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']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 156, 113, 44, 10, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 201, 201, 201, 156, 156, 115, 115, 10, 1, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 682
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078645 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078645
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078645/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078645
Building REAL300000078646
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078646'
/scratch/stefan/7769659/working/building/REAL300000078646 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078646

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078646/0 /scratch/stefan/7769659/working/building/REAL300000078646 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/638
`/scratch/stefan/7769659/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1O)

`REAL300000078646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078646 none CSCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 151, 118, 51, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 151, 151, 118, 118, 13, 1, 1, 2] 402
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 630
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078646 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078646/1 /scratch/stefan/7769659/working/building/REAL300000078646 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/639
`/scratch/stefan/7769659/working/3D/639' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-])

`REAL300000078646.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078646/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078646 none CSCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 98, 77, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 98, 98, 77, 77, 6, 1, 1] 117
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078646 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078646
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078646/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078646/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078646
Building REAL300000078647
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078647'
/scratch/stefan/7769659/working/building/REAL300000078647 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078647

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078647/0 /scratch/stefan/7769659/working/building/REAL300000078647 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/640
`/scratch/stefan/7769659/working/3D/640' -> `0.mol2'
Preparing input files

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

`REAL300000078647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078647 none COC1=CC(Br)=CC(C=NOCCSC)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 57, 73, 105, 1, 1, 2, 10, 21, 21, 3, 3, 3, 1, 1, 4, 57, 57, 73, 73, 105, 105, 105, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 389
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078647 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078647
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078647/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078647
Building REAL300000078648
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078648'
/scratch/stefan/7769659/working/building/REAL300000078648 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078648

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078648/0 /scratch/stefan/7769659/working/building/REAL300000078648 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/641
`/scratch/stefan/7769659/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078648 none CSCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 151, 104, 46, 24, 24, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 151, 151, 104, 104, 24, 16, 16, 9, 9, 1, 1, 16, 16] 201
rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 701
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078648 none CSCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 39, 24, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 1, 1, 86, 86, 86, 39, 39, 24, 24, 4, 1, 1, 2, 2, 16, 16, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 21, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078648 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078648
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078648/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078648
Building REAL300000078649
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078649'
/scratch/stefan/7769659/working/building/REAL300000078649 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078649

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078649/0 /scratch/stefan/7769659/working/building/REAL300000078649 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/642
`/scratch/stefan/7769659/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC(I)=CC(C(=O)[O-])=C1)

`REAL300000078649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078649 none CSCCON=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 117, 37, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 154, 154, 118, 118, 12, 1, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 666
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078649 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078649
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078649/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078649
Building REAL300000078650
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078650'
/scratch/stefan/7769659/working/building/REAL300000078650 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078650

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078650/0 /scratch/stefan/7769659/working/building/REAL300000078650 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/643
`/scratch/stefan/7769659/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21)

`REAL300000078650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078650 none CSCCON=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 171, 130, 51, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 171, 171, 130, 130, 11, 2, 1, 1, 1, 1, 1] 402
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078650 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078650
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078650/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078650
Building REAL300000078651
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078651'
/scratch/stefan/7769659/working/building/REAL300000078651 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078651

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078651/0 /scratch/stefan/7769659/working/building/REAL300000078651 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/644
`/scratch/stefan/7769659/working/3D/644' -> `0.mol2'
Preparing input files

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

`REAL300000078651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078651 none CSCCON=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 93, 67, 23, 11, 11, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 146, 146, 146, 93, 93, 67, 67, 11, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201
rigid atoms, others: [33, 34, 35, 38, 10, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 39, 40])
total number of confs: 485
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078651 none CSCCON=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 38, 27, 7, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 21, 21, 5, 1, 1, 61, 61, 61, 37, 37, 27, 27, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 40, 21, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078651 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078651
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078651/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078651
Building REAL300000078652
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078652'
/scratch/stefan/7769659/working/building/REAL300000078652 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078652

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078652/0 /scratch/stefan/7769659/working/building/REAL300000078652 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/645
`/scratch/stefan/7769659/working/3D/645' -> `0.mol2'
Preparing input files

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

`REAL300000078652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078652 none CCOC1=CC(C=NOCCSC)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 14, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 2, 2, 6, 22, 25, 39, 1, 1, 1, 1, 7, 20, 32, 32, 3, 3, 3, 3, 3, 1, 2, 22, 22, 24, 24, 39, 39, 39, 1, 1, 20, 20] 201
rigid atoms, others: [2, 3, 4, 5, 6, 13, 14, 15, 16, 35, 36, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078652 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078652
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078652/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078652
Building REAL300000078653
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078653'
/scratch/stefan/7769659/working/building/REAL300000078653 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078653

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078653/0 /scratch/stefan/7769659/working/building/REAL300000078653 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/646
`/scratch/stefan/7769659/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-])

`REAL300000078653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078653 none CSCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 12, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 153, 124, 62, 23, 23, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 201, 201, 201, 153, 153, 124, 124, 23, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 606
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078653 none CSCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 12, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 72, 51, 18, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 113, 113, 113, 72, 72, 51, 51, 4, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [6, 7, 8, 9, 10, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078653 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078653
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078653/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078653
Building REAL300000078654
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078654'
/scratch/stefan/7769659/working/building/REAL300000078654 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078654

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078654/0 /scratch/stefan/7769659/working/building/REAL300000078654 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/647
`/scratch/stefan/7769659/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21)

`REAL300000078654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078654 none CSCCON=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 24, 20, 9, 4, 4, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 24, 24, 20, 20, 4, 2, 2, 2, 1, 1, 1] 38
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078654 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078654
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078654/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078654
Building REAL300000078655
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078655'
/scratch/stefan/7769659/working/building/REAL300000078655 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078655

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078655/0 /scratch/stefan/7769659/working/building/REAL300000078655 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/648
`/scratch/stefan/7769659/working/3D/648' -> `0.mol2'
Preparing input files

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

`REAL300000078655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078655 none CSCCON=C(C)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 136, 109, 32, 10, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 136, 136, 109, 109, 10, 10, 10, 1, 1, 1, 1] 185
rigid atoms, others: [32, 33, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078655 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078655
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078655/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078655
Building REAL300000078656
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078656'
/scratch/stefan/7769659/working/building/REAL300000078656 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078656

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078656/0 /scratch/stefan/7769659/working/building/REAL300000078656 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/649
`/scratch/stefan/7769659/working/3D/649' -> `0.mol2'
Preparing input files

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

`REAL300000078656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078656 none CSCCON=CC1=C(C(=O)[O-])C=C(Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 100, 74, 26, 10, 10, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 146, 146, 146, 100, 100, 74, 74, 10, 1] 146
rigid atoms, others: [6, 7, 8, 9, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078656 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078656
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078656/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078656
Building REAL300000078657
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078657'
/scratch/stefan/7769659/working/building/REAL300000078657 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078657

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078657/0 /scratch/stefan/7769659/working/building/REAL300000078657 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/650
`/scratch/stefan/7769659/working/3D/650' -> `0.mol2'
Preparing input files

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

`REAL300000078657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078657 none CSCCON=C(C)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 144, 108, 32, 7, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 144, 144, 108, 108, 7, 7, 7, 1, 1, 1, 1, 1] 169
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 615
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078657 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078657
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078657/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078657
Building REAL300000078658
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078658'
/scratch/stefan/7769659/working/building/REAL300000078658 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078658

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078658/0 /scratch/stefan/7769659/working/building/REAL300000078658 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/651
`/scratch/stefan/7769659/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)

`REAL300000078658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078658 none CSCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 126, 126, 52, 44, 44, 44, 44, 44, 44, 44, 44, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 126, 126, 126, 126, 44, 44, 44, 44, 44, 6, 6, 1, 1] 201
rigid atoms, others: [37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078658 none CSCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 12, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 12, 12, 12, 12, 2, 1, 1, 1, 1, 18, 18, 44, 44] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078658 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078658
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078658/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078658
Building REAL300000078659
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078659'
/scratch/stefan/7769659/working/building/REAL300000078659 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078659

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078659/0 /scratch/stefan/7769659/working/building/REAL300000078659 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/652
`/scratch/stefan/7769659/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=CC(Br)=C1C(=O)[O-])

`REAL300000078659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078659 none CSCCON=CC1=CC=CC(Br)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 18, 16, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 33, 33, 33, 18, 18, 16, 16, 4, 1, 1, 1] 33
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078659 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078659
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078659/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078659
Building REAL300000078660
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078660'
/scratch/stefan/7769659/working/building/REAL300000078660 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078660

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078660/0 /scratch/stefan/7769659/working/building/REAL300000078660 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/653
`/scratch/stefan/7769659/working/3D/653' -> `0.mol2'
Preparing input files

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

`REAL300000078660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078660 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NOCCSC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 12, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 29, 103, 140, 197, 3, 3, 3, 1, 4, 4, 4, 1, 1, 7, 103, 103, 140, 140, 197, 197, 197] 201
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 26, 30, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078660 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078660
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078660/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078660
Building REAL300000078661
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078661'
/scratch/stefan/7769659/working/building/REAL300000078661 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078661

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078661/0 /scratch/stefan/7769659/working/building/REAL300000078661 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/654
`/scratch/stefan/7769659/working/3D/654' -> `0.mol2'
Preparing input files

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

`REAL300000078661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078661 none CSCCON=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 48, 35, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 16, 26, 26, 1, 1, 1, 90, 90, 90, 47, 47, 36, 36, 5, 1, 1, 16, 16, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 18, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078661 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078661
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078661/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078661
Building REAL300000078662
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078662'
/scratch/stefan/7769659/working/building/REAL300000078662 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078662

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078662/0 /scratch/stefan/7769659/working/building/REAL300000078662 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/655
`/scratch/stefan/7769659/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000078662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078662 none CSCCON=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 38, 32, 8, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 21, 32, 32, 1, 1, 84, 84, 84, 37, 37, 32, 32, 3, 1, 1, 8, 21, 21, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078662 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078662
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078662/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078662
Building REAL300000078663
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078663'
/scratch/stefan/7769659/working/building/REAL300000078663 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078663

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078663/0 /scratch/stefan/7769659/working/building/REAL300000078663 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/656
`/scratch/stefan/7769659/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCON=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F)

`REAL300000078663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078663 none CSCCON=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 122, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 159, 159, 122, 122, 12, 1, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 667
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078663 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078663
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078663/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078663
Building REAL300000078664
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078664'
/scratch/stefan/7769659/working/building/REAL300000078664 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078664

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078664/0 /scratch/stefan/7769659/working/building/REAL300000078664 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/657
`/scratch/stefan/7769659/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)

`REAL300000078664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078664 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=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', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 6, 1, 1, 1, 14, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078664 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=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', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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, 4, 4, 9, 14, 14, 14, 9, 14, 14, 14, 1, 1, 1, 1, 4, 9, 14, 14, 14, 1, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078664 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078664
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078664/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078664
Building REAL300000078665
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078665'
/scratch/stefan/7769659/working/building/REAL300000078665 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078665

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078665/0 /scratch/stefan/7769659/working/building/REAL300000078665 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/658
`/scratch/stefan/7769659/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078665 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 142, 62, 62, 62, 34, 62, 62, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 62, 62, 62, 62, 33, 7, 1, 1, 1] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 639
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078665 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 81, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 56, 56, 56, 22, 56, 56, 56, 44, 44, 1, 1, 1, 1, 6, 22, 56, 22, 56] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 436
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078665 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078665
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078665/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078665
Building REAL300000078666
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078666'
/scratch/stefan/7769659/working/building/REAL300000078666 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078666

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078666/0 /scratch/stefan/7769659/working/building/REAL300000078666 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/659
`/scratch/stefan/7769659/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)

`REAL300000078666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078666 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 141, 32, 32, 97, 97, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 97, 97, 32, 7, 1, 1, 1, 97, 97] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 721
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078666 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 36, 3, 1, 1, 1, 1, 1, 1, 10, 10, 40, 88, 88, 88, 45, 88, 88, 88, 1, 1, 16, 16, 1, 1, 10, 40, 88, 88, 88, 1, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 429
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078666 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078666
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078666/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078666
Building REAL300000078667
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078667'
/scratch/stefan/7769659/working/building/REAL300000078667 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078667

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078667/0 /scratch/stefan/7769659/working/building/REAL300000078667 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/660
`/scratch/stefan/7769659/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)C(=O)[O-])

`REAL300000078667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078667 none CC(OC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 159, 59, 59, 59, 59, 59, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 24, 4, 1, 1, 1, 59] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 451
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078667 none CC(OC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 11, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 59, 59, 59, 30, 59, 59, 59, 1, 32, 46, 46, 32, 32, 32, 32, 1, 1, 1, 9, 29, 59, 29, 59, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 19, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 332
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078667 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078667
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078667/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078667
Building REAL300000078668
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078668'
/scratch/stefan/7769659/working/building/REAL300000078668 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078668

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078668/0 /scratch/stefan/7769659/working/building/REAL300000078668 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/661
`/scratch/stefan/7769659/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078668 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 198, 181, 110, 41, 41, 41, 41, 41, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 201, 201, 181, 181, 41, 42, 42, 14, 4, 1, 1, 1, 41] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 629
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078668 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 37, 47, 24, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 57, 57, 57, 26, 57, 57, 57, 1, 37, 37, 24, 24, 1, 1, 1, 6, 25, 57, 26, 57, 1] 201
rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 382
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078668 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078668
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078668/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078668
Building REAL300000078669
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078669'
/scratch/stefan/7769659/working/building/REAL300000078669 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078669

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078669/0 /scratch/stefan/7769659/working/building/REAL300000078669 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/662
`/scratch/stefan/7769659/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1[N+](=O)[O-])

`REAL300000078669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078669 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 16, 16, 21, 21, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 4, 1, 1, 1, 21] 21
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078669 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 26, 45, 7, 1, 1, 1, 1, 1, 1, 13, 13, 40, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 2, 2, 26, 26, 1, 1, 13, 40, 77, 77, 77, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078669 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078669
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078669/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078669
Building REAL300000078670
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078670'
/scratch/stefan/7769659/working/building/REAL300000078670 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078670

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078670/0 /scratch/stefan/7769659/working/building/REAL300000078670 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/663
`/scratch/stefan/7769659/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078670 none O=C([O-])COC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 148, 70, 70, 70, 70, 70, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 70, 70, 70, 31, 8, 1, 1, 1, 70] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 511
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078670 none O=C([O-])COC1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 42, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 68, 68, 68, 31, 68, 68, 68, 1, 24, 24, 1, 1, 1, 10, 30, 68, 31, 68, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 21, 24, 25, 26] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 334
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078670 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078670
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078670/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078670
Building REAL300000078671
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078671'
/scratch/stefan/7769659/working/building/REAL300000078671 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078671

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078671/0 /scratch/stefan/7769659/working/building/REAL300000078671 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/664
`/scratch/stefan/7769659/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(OCC(=O)[O-])=C1)

`REAL300000078671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078671 none COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 37, 37, 37, 37, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 105, 195, 201, 201, 37, 61, 61, 61, 37, 37, 19, 7, 1, 1, 1, 195, 195, 37] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 662
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078671 none COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 16, 36, 36, 36, 16, 36, 36, 36, 1, 1, 9, 42, 81, 81, 1, 3, 3, 3, 1, 1, 4, 16, 36, 16, 36, 42, 42, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 371
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078671 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078671
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078671/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078671
Building REAL300000078672
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078672'
/scratch/stefan/7769659/working/building/REAL300000078672 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078672

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078672/0 /scratch/stefan/7769659/working/building/REAL300000078672 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/665
`/scratch/stefan/7769659/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)

`REAL300000078672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078672 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 201, 201, 119, 201, 200, 19, 19, 58, 58, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 19, 5, 1, 1, 1, 58, 58] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 675
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078672 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [52, 32, 52, 7, 32, 32, 1, 1, 1, 1, 1, 1, 6, 6, 23, 53, 53, 53, 24, 53, 53, 53, 1, 1, 1, 1, 6, 23, 53, 53, 53, 1, 1] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078672 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078672
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078672/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078672
Building REAL300000078673
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078673'
/scratch/stefan/7769659/working/building/REAL300000078673 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078673

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078673/0 /scratch/stefan/7769659/working/building/REAL300000078673 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/666
`/scratch/stefan/7769659/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078673 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 26, 8, 1, 1, 1] 36
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078673 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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, 2, 2, 1, 1, 1, 1, 1, 9, 9, 29, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 9, 29, 36, 36, 36] 36
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 24] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29])
total number of confs: 90
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078673 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078673
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078673/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078673
Building REAL300000078674
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078674'
/scratch/stefan/7769659/working/building/REAL300000078674 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078674

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078674/0 /scratch/stefan/7769659/working/building/REAL300000078674 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/667
`/scratch/stefan/7769659/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)

`REAL300000078674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078674 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 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, 40, 40, 40, 40, 40, 40, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 25, 6, 1, 1, 1, 40, 40] 40
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078674 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 25, 40, 40, 40, 31, 40, 40, 40, 1, 1, 4, 4, 4, 1, 9, 25, 40, 40, 40, 1, 1] 40
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 23, 24, 28] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078674 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078674
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078674/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078674
Building REAL300000078675
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078675'
/scratch/stefan/7769659/working/building/REAL300000078675 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078675

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078675/0 /scratch/stefan/7769659/working/building/REAL300000078675 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/668
`/scratch/stefan/7769659/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC(Cl)=CC(Cl)=C3)=C2C=C1)

`REAL300000078675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078675 none O=C([O-])C1=CC2=NNC(C=NNC3=CC(Cl)=CC(Cl)=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 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, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 17, 9, 1, 1, 1, 20, 20] 20
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078675 none O=C([O-])C1=CC2=NNC(C=NNC3=CC(Cl)=CC(Cl)=C3)=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 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, 1, 1, 6, 6, 16, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 16, 20, 20, 20, 1, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078675 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078675/1 /scratch/stefan/7769659/working/building/REAL300000078675 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/669
`/scratch/stefan/7769659/working/3D/669' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=NNC2=C1)

`REAL300000078675.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078675/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078675 none O=C([O-])C1=CC=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 40, 41, 40, 40, 40, 40, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 26, 9, 1, 1, 1, 40, 40] 41
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 72
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078675 none O=C([O-])C1=CC=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=NNC2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 36, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 10, 36, 41, 41, 41, 1, 1] 41
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078675 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078675
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078675/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078675/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078675
Building REAL300000078676
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078676'
/scratch/stefan/7769659/working/building/REAL300000078676 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078676

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078676/0 /scratch/stefan/7769659/working/building/REAL300000078676 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/670
`/scratch/stefan/7769659/working/3D/670' -> `0.mol2'
Preparing input files

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

`REAL300000078676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078676 none O=C([O-])CN1C=C(CN=NC2=CC(Cl)=CC(Cl)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 105, 105, 105, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 105, 28, 28, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 657
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078676 none O=C([O-])CN1C=C(CN=NC2=CC(Cl)=CC(Cl)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 12, 1, 1, 1, 1, 1, 9, 73, 73, 100, 100, 100, 73, 100, 100, 100, 1, 1, 6, 6, 1, 9, 9, 100, 73, 100] 201
rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078676 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078676/1 /scratch/stefan/7769659/working/building/REAL300000078676 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/671
`/scratch/stefan/7769659/working/3D/671' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N=N1)

`REAL300000078676.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078676/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078676 none O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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, 30, 30, 30, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 49, 49, 30, 18, 6, 1, 1, 1] 49
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078676 none O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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: [11, 7, 11, 1, 1, 1, 1, 1, 4, 4, 16, 29, 29, 29, 17, 29, 29, 29, 1, 1, 7, 7, 1, 4, 16, 29, 19, 29] 49
rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078676 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078676
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078676/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078676/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078676
Building REAL300000078677
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078677'
/scratch/stefan/7769659/working/building/REAL300000078677 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078677

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078677/0 /scratch/stefan/7769659/working/building/REAL300000078677 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/672
`/scratch/stefan/7769659/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCCC(=O)[O-])

`REAL300000078677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078677 none COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 52, 52, 52, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 51, 51, 130, 188, 190, 201, 191, 82, 82, 82, 52, 13, 5, 1, 1, 1, 52, 52, 188, 188, 190, 190] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 600
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078677 none COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 17, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 9, 33, 37, 64, 57, 4, 4, 4, 1, 7, 17, 38, 38, 38, 1, 1, 33, 33, 37, 37] 201
rigid atoms, others: [19, 1, 2, 3, 4, 5, 34, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 307
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078677 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078677
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078677/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078677
Building REAL300000078678
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078678'
/scratch/stefan/7769659/working/building/REAL300000078678 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078678

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078678/0 /scratch/stefan/7769659/working/building/REAL300000078678 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/673
`/scratch/stefan/7769659/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(Cl)=C1)

`REAL300000078678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078678 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 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, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 18, 8, 1, 1, 1, 22] 22
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078678 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 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, 8, 8, 18, 22, 22, 22, 18, 22, 22, 22, 1, 1, 1, 1, 1, 8, 18, 22, 18, 22, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078678 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078678
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078678/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078678
Building REAL300000078679
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078679'
/scratch/stefan/7769659/working/building/REAL300000078679 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078679

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078679/0 /scratch/stefan/7769659/working/building/REAL300000078679 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/674
`/scratch/stefan/7769659/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1O)

`REAL300000078679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078679 none O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [25, 24, 25, 24, 24, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 19, 6, 1, 1, 1, 24, 24, 48] 50
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078679 none O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 17, 25, 25, 25, 22, 25, 25, 25, 1, 1, 1, 1, 1, 6, 17, 25, 25, 25, 1, 1, 2] 50
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 29])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078679 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078679
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078679/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078679
Building REAL300000078680
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078680'
/scratch/stefan/7769659/working/building/REAL300000078680 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078680

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078680/0 /scratch/stefan/7769659/working/building/REAL300000078680 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/675
`/scratch/stefan/7769659/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)C(=O)[O-])

`REAL300000078680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078680 none CC(OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [199, 139, 31, 31, 89, 89, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 199, 200, 200, 199, 199, 199, 199, 89, 89, 31, 6, 1, 1, 1, 89, 89] 200
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 712
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078680 none CC(OC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 1, 1, 1, 1, 1, 9, 9, 43, 96, 96, 96, 50, 96, 96, 96, 1, 1, 20, 30, 30, 20, 20, 20, 20, 1, 1, 9, 43, 96, 96, 96, 1, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 18, 19, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 441
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078680 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078680
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078680/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078680
Building REAL300000078681
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078681'
/scratch/stefan/7769659/working/building/REAL300000078681 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078681

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078681/0 /scratch/stefan/7769659/working/building/REAL300000078681 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/676
`/scratch/stefan/7769659/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C2=CC=CC=C21)

`REAL300000078681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078681 none O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 83, 83, 83, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 84, 84, 84, 84, 83, 125, 125, 83, 29, 6, 1, 1, 1, 84, 84, 84, 83] 125
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 335
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078681 none O=C([O-])CN1C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 8, 16, 1, 1, 1, 1, 1, 10, 10, 48, 80, 80, 80, 55, 80, 80, 80, 1, 1, 1, 1, 1, 1, 8, 8, 1, 10, 48, 80, 56, 80, 1, 1, 1, 1] 124
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 26, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078681 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078681
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078681/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078681
Building REAL300000078682
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078682'
/scratch/stefan/7769659/working/building/REAL300000078682 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078682

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078682/0 /scratch/stefan/7769659/working/building/REAL300000078682 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/677
`/scratch/stefan/7769659/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N1)

`REAL300000078682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078682 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 20, 8, 1, 1, 1, 28] 28
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 50
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078682 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC(Cl)=CC(Cl)=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 19, 28, 28, 28, 19, 28, 28, 28, 1, 2, 2, 2, 1, 6, 18, 28, 19, 28, 1] 28
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078682 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078682
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078682/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078682
Building REAL300000078683
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078683'
/scratch/stefan/7769659/working/building/REAL300000078683 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078683

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078683/0 /scratch/stefan/7769659/working/building/REAL300000078683 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/678
`/scratch/stefan/7769659/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078683 none O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 19, 20, 20, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 19, 20, 20, 17, 7, 1, 1, 1, 20] 20
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078683 none O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 18, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078683 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078683
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078683/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078683
Building REAL300000078684
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078684'
/scratch/stefan/7769659/working/building/REAL300000078684 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078684

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078684/0 /scratch/stefan/7769659/working/building/REAL300000078684 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/679
`/scratch/stefan/7769659/working/3D/679' -> `0.mol2'
Preparing input files

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

`REAL300000078684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078684 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 23, 31, 31, 31, 23, 31, 31, 31, 1, 1, 1, 1, 1, 1, 7, 26, 39, 57, 77, 77, 1, 11, 11, 11, 23, 31, 31, 31, 1, 1, 1, 26, 26, 39, 39, 57, 57, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 12, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 416
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078684 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 25, 25, 73, 125, 162, 201, 201, 201, 25, 8, 8, 8, 3, 1, 1, 1, 25, 25, 25, 125, 125, 162, 162, 201, 201, 25] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 764
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078684 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078684
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078684/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078684
Building REAL300000078685
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078685'
/scratch/stefan/7769659/working/building/REAL300000078685 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078685

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078685/0 /scratch/stefan/7769659/working/building/REAL300000078685 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/680
`/scratch/stefan/7769659/working/3D/680' -> `0.mol2'
Preparing input files

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

`REAL300000078685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078685 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 5, 24, 57, 61, 61, 61, 61, 61, 173, 201, 201, 201, 201, 61, 61, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 60, 60, 60, 61, 61, 61, 201, 201, 201, 201, 61, 61, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 577
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078685 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 2, 1, 1, 1, 1, 1, 1, 11, 27, 27, 35, 35, 1, 1, 9, 39, 39, 58, 58, 58, 39, 58, 58, 58, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 58, 39, 58] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 14, 15, 40, 35] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42, 43, 44])
total number of confs: 260
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078685 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078685
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078685/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078685
Building REAL300000078686
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078686'
/scratch/stefan/7769659/working/building/REAL300000078686 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078686

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078686/0 /scratch/stefan/7769659/working/building/REAL300000078686 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/681
`/scratch/stefan/7769659/working/3D/681' -> `0.mol2'
Preparing input files

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

`REAL300000078686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078686 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 4, 21, 55, 61, 61, 61, 61, 61, 155, 201, 201, 201, 61, 61, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 59, 59, 59, 61, 61, 61, 201, 201, 61, 61, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 634
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078686 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 2, 1, 1, 1, 1, 1, 1, 6, 22, 35, 35, 1, 1, 9, 42, 42, 57, 57, 57, 42, 57, 57, 57, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 22, 22, 1, 1, 57, 42, 57] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 13, 14, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41])
total number of confs: 247
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078686 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078686
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078686/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078686
Building REAL300000078687
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078687'
/scratch/stefan/7769659/working/building/REAL300000078687 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078687

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078687/0 /scratch/stefan/7769659/working/building/REAL300000078687 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/682
`/scratch/stefan/7769659/working/3D/682' -> `0.mol2'
Preparing input files

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

`REAL300000078687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078687 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 29, 56, 56, 56, 29, 56, 56, 56, 1, 1, 1, 1, 1, 1, 11, 26, 26, 40, 40, 1, 11, 11, 11, 29, 56, 56, 56, 1, 1, 1, 26, 26, 26, 26, 1] 201
rigid atoms, others: [32, 1, 38, 33, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078687 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 66, 66, 66, 66, 66, 171, 201, 201, 201, 201, 66, 25, 25, 25, 5, 1, 1, 1, 66, 66, 66, 201, 201, 201, 201, 66] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 416
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078687 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078687
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078687/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078687
Building REAL300000078688
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078688'
/scratch/stefan/7769659/working/building/REAL300000078688 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078688

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078688/0 /scratch/stefan/7769659/working/building/REAL300000078688 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/683
`/scratch/stefan/7769659/working/3D/683' -> `0.mol2'
Preparing input files

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

`REAL300000078688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078688 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 5, 27, 53, 60, 60, 60, 60, 60, 187, 201, 201, 201, 199, 60, 60, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 58, 58, 59, 60, 60, 60, 201, 201, 201, 201, 60, 60, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 518
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078688 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 4, 1, 1, 1, 1, 1, 1, 6, 17, 17, 29, 25, 1, 1, 10, 45, 45, 61, 61, 61, 45, 61, 61, 61, 10, 10, 10, 10, 5, 5, 4, 4, 1, 1, 17, 17, 17, 17, 1, 1, 61, 45, 61] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 14, 15, 40, 35] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42, 43, 44])
total number of confs: 242
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078688 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078688
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078688/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078688
Building REAL300000078689
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078689'
/scratch/stefan/7769659/working/building/REAL300000078689 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078689

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078689/0 /scratch/stefan/7769659/working/building/REAL300000078689 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/684
`/scratch/stefan/7769659/working/3D/684' -> `0.mol2'
Preparing input files

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

`REAL300000078689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078689 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [12, 1, 12, 12, 38, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 38, 48, 48, 48, 1, 1] 48
rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 118
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078689 none CC(=NNC1=CC(Cl)=CC(Cl)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 7, 1, 1, 1, 50, 50] 50
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28])
total number of confs: 83
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078689 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078689
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078689/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078689
Building REAL300000078690
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078690'
/scratch/stefan/7769659/working/building/REAL300000078690 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078690

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078690/0 /scratch/stefan/7769659/working/building/REAL300000078690 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/685
`/scratch/stefan/7769659/working/3D/685' -> `0.mol2'
Preparing input files

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

`REAL300000078690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078690 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC(Cl)=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 33, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 6, 6] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 60
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078690 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC(Cl)=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 13, 13, 24, 24, 24, 24, 24, 24, 24, 1, 6, 6, 2, 6, 6, 1, 1, 1, 24, 24, 24, 1, 1] 35
rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 22, 28, 29, 30] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 53
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078690 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC(Cl)=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 26, 31, 26, 26, 35, 35, 31, 35, 35, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 35, 35, 33, 35, 35, 26, 26, 26, 1, 1, 1, 26, 26] 35
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 107
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078690 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078690
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078690/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078690
Building REAL300000078691
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078691'
/scratch/stefan/7769659/working/building/REAL300000078691 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078691

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078691/0 /scratch/stefan/7769659/working/building/REAL300000078691 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/686
`/scratch/stefan/7769659/working/3D/686' -> `0.mol2'
Preparing input files

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

`REAL300000078691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078691 none CC(N=NC1=CC(Cl)=CC(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 25, 25, 42, 42, 42, 27, 42, 42, 42, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 42, 31, 42, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 65
rigid atoms, others: [32, 1, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078691 none CC(N=NC1=CC(Cl)=CC(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 41, 41, 41, 41, 41, 64, 64, 64, 41, 41, 41, 28, 28, 28, 28, 1, 1, 1, 41, 41, 64, 64, 41, 41, 41, 41, 41, 41] 64
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078691 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078691
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078691/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078691
Building REAL300000078692
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078692'
/scratch/stefan/7769659/working/building/REAL300000078692 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078692

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078692/0 /scratch/stefan/7769659/working/building/REAL300000078692 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/687
`/scratch/stefan/7769659/working/3D/687' -> `0.mol2'
Preparing input files

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

`REAL300000078692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078692 none CC(CCCCCCC(=O)[O-])N=NC1=CC(Cl)=CC(Cl)=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', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 27, 57, 67, 80, 108, 121, 200, 201, 201, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 61, 61, 67, 64, 85, 85, 108, 104, 127, 127, 199, 197, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 992
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078692 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078692
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078692/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078692
Building REAL300000078693
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078693'
/scratch/stefan/7769659/working/building/REAL300000078693 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078693

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078693/0 /scratch/stefan/7769659/working/building/REAL300000078693 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/688
`/scratch/stefan/7769659/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078693 none CC1C(CC(=O)[O-])CCC1N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 26, 26, 26, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 26, 26, 17, 17, 17, 17, 17, 1, 1, 1] 26
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078693 none CC1C(CC(=O)[O-])CCC1N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 12, 12, 1, 1, 1, 1, 8, 8, 15, 15, 15, 8, 15, 15, 15, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 15, 11, 15] 26
rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 23, 24, 27, 28, 29, 30, 31] set([32, 33, 34, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078693 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078693
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078693/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078693
Building REAL300000078694
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078694'
/scratch/stefan/7769659/working/building/REAL300000078694 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078694

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078694/0 /scratch/stefan/7769659/working/building/REAL300000078694 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/689
`/scratch/stefan/7769659/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078694 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 6, 24, 37, 47, 47, 47, 47, 47, 47, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 37, 37, 47, 47, 47, 47, 47, 47, 1, 1, 1] 47
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 183
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078694 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 7, 1, 1, 1, 3, 3, 1, 1, 1, 12, 39, 39, 47, 47, 47, 44, 47, 47, 47, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 47, 44, 47] 47
rigid atoms, others: [2, 3, 4, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078694 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078694
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078694/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078694
Building REAL300000078695
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078695'
/scratch/stefan/7769659/working/building/REAL300000078695 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078695

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078695/0 /scratch/stefan/7769659/working/building/REAL300000078695 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/690
`/scratch/stefan/7769659/working/3D/690' -> `0.mol2'
Preparing input files

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

`REAL300000078695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078695 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC(Cl)=CC(Cl)=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 6, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 64, 64, 64, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 64, 64] 64
rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078695 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC(Cl)=CC(Cl)=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 34, 34, 47, 47, 47, 34, 47, 47, 47, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 47, 34, 47, 2, 2] 64
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078695 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078695
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078695/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078695
Building REAL300000078696
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078696'
/scratch/stefan/7769659/working/building/REAL300000078696 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078696

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078696/0 /scratch/stefan/7769659/working/building/REAL300000078696 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/691
`/scratch/stefan/7769659/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078696 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 29, 11, 1, 1, 1] 46
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078696 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 34, 46, 46, 46, 41, 46, 46, 46, 2, 2, 2, 1, 2, 2, 2, 1, 12, 34, 46, 46, 46] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078696 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078696
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078696/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078696
Building REAL300000078697
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078697'
/scratch/stefan/7769659/working/building/REAL300000078697 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078697

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078697/0 /scratch/stefan/7769659/working/building/REAL300000078697 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/692
`/scratch/stefan/7769659/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1Cl)

`REAL300000078697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078697 none O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 16, 6, 1, 1, 1] 19
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078697 none O=C([O-])C1=CC=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 13, 19, 19, 19, 13, 19, 19, 19, 1, 1, 1, 1, 1, 5, 13, 19, 13, 19] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078697 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078697
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078697/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078697
Building REAL300000078698
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078698'
/scratch/stefan/7769659/working/building/REAL300000078698 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078698

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078698/0 /scratch/stefan/7769659/working/building/REAL300000078698 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/693
`/scratch/stefan/7769659/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1F)

`REAL300000078698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078698 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 49, 50, 49, 49, 49, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 27, 7, 1, 1, 1, 49] 50
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078698 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 22, 51, 51, 51, 23, 51, 51, 51, 1, 1, 1, 1, 1, 6, 22, 51, 27, 51, 1] 51
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078698 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078698
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078698/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078698
Building REAL300000078699
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078699'
/scratch/stefan/7769659/working/building/REAL300000078699 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078699

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078699/0 /scratch/stefan/7769659/working/building/REAL300000078699 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/694
`/scratch/stefan/7769659/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)O1)

`REAL300000078699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078699 none O=C([O-])C=CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 47, 47, 47, 47, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 81, 81, 47, 47, 29, 6, 1, 1, 1] 81
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078699 none O=C([O-])C=CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 24, 11, 1, 1, 1, 1, 1, 1, 6, 6, 21, 46, 46, 46, 21, 46, 46, 46, 1, 11, 11, 1, 1, 6, 21, 46, 21, 46] 79
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078699 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078699/1 /scratch/stefan/7769659/working/building/REAL300000078699 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/695
`/scratch/stefan/7769659/working/3D/695' -> `1.mol2'
Preparing input files

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

`REAL300000078699.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078699/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078699 none O=C([O-])C=CC1=CC=C(CN=NC2=CC(Cl)=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 201, 197, 95, 95, 95, 95, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 197, 197, 95, 95, 33, 33, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 523
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078699 none O=C([O-])C=CC1=CC=C(CN=NC2=CC(Cl)=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 10, 24, 10, 1, 1, 1, 1, 1, 1, 8, 69, 69, 91, 91, 92, 69, 91, 91, 91, 1, 10, 10, 1, 1, 8, 8, 92, 69, 91] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078699 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078699
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078699/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078699/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078699
Building REAL300000078700
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078700'
/scratch/stefan/7769659/working/building/REAL300000078700 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078700

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078700/0 /scratch/stefan/7769659/working/building/REAL300000078700 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/696
`/scratch/stefan/7769659/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1)

`REAL300000078700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078700 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 13, 7, 1, 1, 1, 19] 19
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078700 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 19, 19, 19, 14, 19, 19, 19, 1, 1, 1, 1, 1, 1, 6, 14, 19, 14, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078700 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078700
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078700/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078700
Building REAL300000078701
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078701'
/scratch/stefan/7769659/working/building/REAL300000078701 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078701

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078701/0 /scratch/stefan/7769659/working/building/REAL300000078701 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/697
`/scratch/stefan/7769659/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=N1)

`REAL300000078701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078701 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 14, 6, 1, 1, 1, 27] 27
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078701 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 6, 18, 27, 27, 27, 18, 27, 27, 27, 1, 1, 1, 1, 6, 18, 27, 18, 27, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078701 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078701
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078701/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078701
Building REAL300000078702
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078702'
/scratch/stefan/7769659/working/building/REAL300000078702 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078702

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078702/0 /scratch/stefan/7769659/working/building/REAL300000078702 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/698
`/scratch/stefan/7769659/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1O)

`REAL300000078702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078702 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [44, 43, 44, 43, 43, 43, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 22, 6, 1, 1, 1, 43, 86] 88
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28, 29])
total number of confs: 165
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078702 none O=C([O-])C1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 23, 44, 44, 44, 24, 44, 44, 44, 1, 1, 1, 1, 1, 7, 23, 44, 24, 44, 1, 2] 88
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 29])
total number of confs: 132
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078702 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078702
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078702/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078702
Building REAL300000078703
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078703'
/scratch/stefan/7769659/working/building/REAL300000078703 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078703

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078703/0 /scratch/stefan/7769659/working/building/REAL300000078703 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/699
`/scratch/stefan/7769659/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1C(=O)[O-])

`REAL300000078703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078703 none CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 6, 1, 1, 1, 32] 32
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 53
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078703 none CC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 32, 32, 32, 23, 32, 32, 32, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 22, 32, 23, 32, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078703 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078703
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078703/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078703
Building REAL300000078704
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078704'
/scratch/stefan/7769659/working/building/REAL300000078704 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078704

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078704/0 /scratch/stefan/7769659/working/building/REAL300000078704 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/700
`/scratch/stefan/7769659/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078704 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 21, 7, 1, 1, 1, 46] 46
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 25])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078704 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 7, 7, 31, 46, 46, 46, 31, 46, 46, 46, 1, 6, 30, 46, 31, 46, 1] 46
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078704 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078704
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078704/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078704
Building REAL300000078705
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078705'
/scratch/stefan/7769659/working/building/REAL300000078705 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078705

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078705/0 /scratch/stefan/7769659/working/building/REAL300000078705 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/701
`/scratch/stefan/7769659/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078705 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [19, 20, 20, 20, 20, 20, 20, 20, 16, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 15, 8, 1, 1, 1] 20
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078705 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 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, 1, 1, 7, 7, 17, 19, 19, 20, 18, 19, 19, 19, 2, 2, 2, 1, 7, 17, 19, 19, 19] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078705 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078705
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078705/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078705
Building REAL300000078706
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078706'
/scratch/stefan/7769659/working/building/REAL300000078706 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078706

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078706/0 /scratch/stefan/7769659/working/building/REAL300000078706 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/702
`/scratch/stefan/7769659/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)O2)=CC=C1O)

`REAL300000078706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078706 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
312  conformations in input
total number of sets (complete confs): 312
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 31, 57, 57, 57, 31, 57, 57, 57, 1, 13, 13, 12, 12, 13, 1, 1, 6, 31, 57, 31, 57, 13, 13, 26] 312
rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078706 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
312  conformations in input
total number of sets (complete confs): 312
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 57, 57, 122, 156, 156, 156, 122, 156, 156, 156, 13, 1, 1, 1, 1, 1, 13, 13, 57, 122, 156, 122, 156, 1, 1, 2] 312
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078706 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
336  conformations in input
total number of sets (complete confs): 336
using faster count positions algorithm for large data
unique positions, atoms: [168, 168, 168, 168, 168, 71, 71, 71, 71, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 168, 168, 168, 168, 168, 71, 71, 34, 8, 1, 1, 1, 168, 168, 336] 336
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: 579
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078706 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078706
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078706/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078706
Building REAL300000078707
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078707'
/scratch/stefan/7769659/working/building/REAL300000078707 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078707

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078707/0 /scratch/stefan/7769659/working/building/REAL300000078707 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/703
`/scratch/stefan/7769659/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078707 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 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: [16, 16, 16, 16, 16, 17, 17, 16, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 16, 16, 15, 7, 1, 1, 1] 17
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078707 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 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, 2, 2, 1, 1, 1, 6, 6, 14, 17, 17, 17, 14, 17, 17, 17, 2, 2, 2, 1, 1, 6, 14, 17, 14, 17] 17
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 23, 24] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078707 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078707
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078707/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078707
Building REAL300000078708
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078708'
/scratch/stefan/7769659/working/building/REAL300000078708 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078708

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078708/0 /scratch/stefan/7769659/working/building/REAL300000078708 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/704
`/scratch/stefan/7769659/working/3D/704' -> `0.mol2'
Preparing input files

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

`REAL300000078708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078708 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1] 12
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 23
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078708 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 21, 30, 30, 30, 21, 30, 30, 30, 3, 3, 3, 3, 3, 3, 1, 1, 1, 10, 21, 30, 21, 30] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 29, 30, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078708 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078708
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078708/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078708
Building REAL300000078709
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078709'
/scratch/stefan/7769659/working/building/REAL300000078709 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078709

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078709/0 /scratch/stefan/7769659/working/building/REAL300000078709 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/705
`/scratch/stefan/7769659/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)S2)=C1)

`REAL300000078709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078709 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 44, 82, 82, 82, 53, 82, 82, 82, 1, 13, 12, 13, 13, 1, 1, 10, 44, 82, 54, 82, 13] 155
rigid atoms, others: [7, 8, 9, 10, 11, 12, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 240
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078709 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 67, 67, 135, 155, 155, 155, 155, 155, 155, 155, 13, 1, 1, 1, 1, 13, 13, 67, 135, 155, 155, 155, 1] 155
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078709 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [149, 149, 149, 149, 149, 149, 149, 82, 82, 82, 82, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 149, 149, 149, 149, 82, 82, 34, 9, 1, 1, 1, 149] 149
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 234
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078709 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078709
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078709/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078709
Building REAL300000078710
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078710'
/scratch/stefan/7769659/working/building/REAL300000078710 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078710

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078710/0 /scratch/stefan/7769659/working/building/REAL300000078710 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/706
`/scratch/stefan/7769659/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078710 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 92, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 37, 11, 1, 1, 1] 92
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078710 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 55, 91, 91, 91, 55, 91, 91, 91, 4, 4, 4, 1, 1, 1, 11, 55, 91, 55, 91] 92
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 26, 27] set([0, 32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078710 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078710
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078710/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078710
Building REAL300000078711
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078711'
/scratch/stefan/7769659/working/building/REAL300000078711 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078711

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078711/0 /scratch/stefan/7769659/working/building/REAL300000078711 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/707
`/scratch/stefan/7769659/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1)

`REAL300000078711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078711 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 12, 7, 1, 1, 1, 19] 19
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])
total number of confs: 36
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078711 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 5, 5, 13, 18, 18, 18, 13, 18, 18, 18, 1, 1, 1, 1, 1, 5, 13, 18, 13, 18, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078711 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078711
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078711/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078711
Building REAL300000078712
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078712'
/scratch/stefan/7769659/working/building/REAL300000078712 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078712

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078712/0 /scratch/stefan/7769659/working/building/REAL300000078712 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/708
`/scratch/stefan/7769659/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078712 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 26, 9, 1, 1, 1, 38] 38
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 28])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078712 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 1, 1, 10, 10, 30, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 10, 30, 37, 37, 37, 1] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078712 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078712
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078712/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078712
Building REAL300000078713
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078713'
/scratch/stefan/7769659/working/building/REAL300000078713 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078713

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078713/0 /scratch/stefan/7769659/working/building/REAL300000078713 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/709
`/scratch/stefan/7769659/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1C(=O)[O-])

`REAL300000078713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078713 none COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 90, 89, 89, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 102, 102, 102, 102, 102, 90, 32, 9, 1, 1, 1, 89, 89] 102
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078713 none COC1=CC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 44, 89, 89, 89, 43, 89, 89, 89, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 43, 89, 45, 89, 1, 1] 102
rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078713 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078713
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078713/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078713
Building REAL300000078714
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078714'
/scratch/stefan/7769659/working/building/REAL300000078714 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078714

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078714/0 /scratch/stefan/7769659/working/building/REAL300000078714 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/710
`/scratch/stefan/7769659/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(F)=C1)

`REAL300000078714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078714 none O=C([O-])C1=CC(F)=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 17, 18, 18, 18, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 17, 6, 1, 1, 1, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078714 none O=C([O-])C1=CC(F)=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 1, 7, 7, 13, 18, 18, 18, 17, 18, 18, 18, 1, 1, 1, 1, 7, 13, 18, 18, 18, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 58
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078714 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078714
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078714/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078714
Building REAL300000078715
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078715'
/scratch/stefan/7769659/working/building/REAL300000078715 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078715

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078715/0 /scratch/stefan/7769659/working/building/REAL300000078715 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/711
`/scratch/stefan/7769659/working/3D/711' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1)

`REAL300000078715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078715 none CC1=C(C(=O)[O-])NC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 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, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 21, 8, 1, 1, 1, 45] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078715 none CC1=C(C(=O)[O-])NC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 27, 44, 44, 44, 27, 44, 44, 44, 1, 2, 2, 2, 1, 9, 27, 44, 27, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078715 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078715
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078715/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078715
Building REAL300000078716
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078716'
/scratch/stefan/7769659/working/building/REAL300000078716 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078716

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078716/0 /scratch/stefan/7769659/working/building/REAL300000078716 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/712
`/scratch/stefan/7769659/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1O)

`REAL300000078716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078716 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 48, 48, 48, 48, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 21, 6, 1, 1, 1, 96] 96
rigid atoms, others: [32, 33, 34, 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, 35])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078716 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC(Cl)=CC(Cl)=C2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 48, 48, 48, 29, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 10, 29, 48, 31, 48, 2] 96
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078716 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078716
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078716/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078716
Building REAL300000078717
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078717'
/scratch/stefan/7769659/working/building/REAL300000078717 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078717

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078717/0 /scratch/stefan/7769659/working/building/REAL300000078717 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/713
`/scratch/stefan/7769659/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C=C2)=C1)

`REAL300000078717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078717 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 41, 65, 65, 65, 41, 65, 65, 65, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 40, 65, 41, 65, 1, 1, 3] 136
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078717 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 60, 86, 86, 86, 63, 86, 86, 84, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 58, 86, 63, 84, 3, 3, 1] 136
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 26, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078717 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [133, 133, 133, 87, 87, 87, 87, 87, 59, 46, 66, 66, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 87, 133, 133, 87, 87, 87, 66, 66, 26, 7, 1, 1, 1, 66, 66, 87] 133
rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 496
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078717 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078717
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078717/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078717
Building REAL300000078718
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078718'
/scratch/stefan/7769659/working/building/REAL300000078718 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078718

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078718/0 /scratch/stefan/7769659/working/building/REAL300000078718 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/714
`/scratch/stefan/7769659/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CS1)

`REAL300000078718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078718 none O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 18, 7, 1, 1, 1, 26] 26
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 25])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078718 none O=C([O-])C1=CC(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 9, 9, 21, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 21, 26, 26, 26, 1] 26
rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078718 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078718
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078718/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078718
Building REAL300000078719
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078719'
/scratch/stefan/7769659/working/building/REAL300000078719 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078719

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078719/0 /scratch/stefan/7769659/working/building/REAL300000078719 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/715
`/scratch/stefan/7769659/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCC(=O)[O-])

`REAL300000078719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078719 none CCOC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 71, 25, 25, 25, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 102, 178, 190, 190, 104, 104, 104, 104, 104, 25, 8, 4, 1, 1, 1, 26, 26, 179, 179] 201
rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 809
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078719 none CCOC1=CC(C=NNC2=CC(Cl)=CC(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 1, 1, 1, 1, 1, 6, 6, 14, 23, 23, 23, 15, 23, 23, 23, 1, 1, 1, 1, 9, 38, 65, 65, 22, 22, 22, 22, 22, 1, 6, 14, 23, 14, 23, 1, 1, 38, 38] 201
rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 19, 20, 36, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39])
total number of confs: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078719 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078719
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078719/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078719
Building REAL300000078720
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078720'
/scratch/stefan/7769659/working/building/REAL300000078720 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078720

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078720/0 /scratch/stefan/7769659/working/building/REAL300000078720 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/716
`/scratch/stefan/7769659/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)O1)

`REAL300000078720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078720 none O=C([O-])CCC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 177, 161, 71, 71, 71, 71, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 185, 185, 161, 161, 71, 71, 39, 10, 1, 1, 1] 185
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 643
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078720 none O=C([O-])CCC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [34, 20, 26, 8, 1, 1, 1, 1, 1, 1, 6, 6, 34, 66, 66, 66, 34, 66, 66, 66, 1, 20, 20, 8, 8, 1, 1, 6, 34, 66, 34, 66] 184
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078720 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078720/1 /scratch/stefan/7769659/working/building/REAL300000078720 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/717
`/scratch/stefan/7769659/working/3D/717' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=CC(Cl)=CC(Cl)=C2)O1)

`REAL300000078720.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078720/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078720 none O=C([O-])CCC1=CC=C(CN=NC2=CC(Cl)=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 188, 163, 71, 71, 71, 71, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 163, 163, 71, 71, 15, 15, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 799
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078720 none O=C([O-])CCC1=CC=C(CN=NC2=CC(Cl)=CC(Cl)=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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 9, 13, 5, 1, 1, 1, 1, 1, 1, 8, 62, 62, 66, 66, 66, 62, 66, 66, 66, 1, 9, 9, 5, 5, 1, 1, 8, 8, 66, 62, 66] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078720 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078720
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078720/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078720/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078720
Building REAL300000078721
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078721'
/scratch/stefan/7769659/working/building/REAL300000078721 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078721

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078721/0 /scratch/stefan/7769659/working/building/REAL300000078721 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/718
`/scratch/stefan/7769659/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=CC=C1)

`REAL300000078721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078721 none O=C([O-])C1=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 16, 7, 1, 1, 1, 28, 28, 28] 28
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 51
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078721 none O=C([O-])C1=C2NC=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 21, 28, 28, 28, 22, 28, 28, 28, 1, 1, 1, 1, 1, 1, 7, 21, 28, 22, 28, 1, 1, 1] 28
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078721 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078721
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078721/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078721
Building REAL300000078722
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078722'
/scratch/stefan/7769659/working/building/REAL300000078722 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078722

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078722/0 /scratch/stefan/7769659/working/building/REAL300000078722 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/719
`/scratch/stefan/7769659/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=C2O1)

`REAL300000078722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078722 none O=C([O-])C1=CC2=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 22, 7, 1, 1, 1, 33, 33] 33
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078722 none O=C([O-])C1=CC2=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 23, 32, 32, 32, 24, 32, 32, 32, 1, 1, 1, 1, 1, 1, 8, 23, 32, 24, 32, 1, 1] 32
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078722 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078722
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078722/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078722
Building REAL300000078723
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078723'
/scratch/stefan/7769659/working/building/REAL300000078723 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078723

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078723/0 /scratch/stefan/7769659/working/building/REAL300000078723 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/720
`/scratch/stefan/7769659/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=CN12)

`REAL300000078723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078723 none O=C([O-])C1=CN=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 17, 7, 1, 1, 1, 18, 18, 18] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078723 none O=C([O-])C1=CN=C2C(C=NNC3=CC(Cl)=CC(Cl)=C3)=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 1, 3, 3, 11, 18, 18, 18, 12, 18, 18, 18, 1, 1, 1, 1, 1, 3, 11, 18, 12, 18, 1, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078723 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078723
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078723/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078723
Building REAL300000078724
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078724'
/scratch/stefan/7769659/working/building/REAL300000078724 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078724

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078724/0 /scratch/stefan/7769659/working/building/REAL300000078724 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/721
`/scratch/stefan/7769659/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1Cl)

`REAL300000078724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078724 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 168, 68, 39, 68, 68, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 201, 201, 68, 68, 23, 6, 1, 1, 1, 68] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078724 none O=C([O-])COC1=CC=C(C=NNC2=CC(Cl)=CC(Cl)=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 38, 63, 9, 1, 1, 1, 1, 1, 1, 6, 6, 28, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 38, 38, 1, 1, 6, 28, 62, 62, 62, 1] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078724 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078724
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078724/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078724
Building REAL300000078725
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078725'
/scratch/stefan/7769659/working/building/REAL300000078725 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078725

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078725/0 /scratch/stefan/7769659/working/building/REAL300000078725 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/722
`/scratch/stefan/7769659/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C(F)=CC=C2S1)

`REAL300000078725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078725 none O=C([O-])C1=CC2=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 39, 40, 39, 39, 39, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 20, 6, 1, 1, 1, 39, 39] 40
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078725 none O=C([O-])C1=CC2=C(C=NNC3=CC(Cl)=CC(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 29, 40, 40, 40, 29, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 9, 29, 40, 30, 40, 1, 1] 40
rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078725 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078725
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078725/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078725
Building REAL300000078726
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078726'
/scratch/stefan/7769659/working/building/REAL300000078726 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078726

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078726/0 /scratch/stefan/7769659/working/building/REAL300000078726 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/723
`/scratch/stefan/7769659/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1)

`REAL300000078726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078726 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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, 32, 32, 32, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 25, 6, 1, 1, 1] 32
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078726 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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, 1, 1, 1, 8, 8, 20, 32, 32, 32, 21, 32, 32, 32, 4, 4, 4, 1, 1, 1, 8, 20, 32, 22, 32] 32
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078726 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078726
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078726/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078726
Building REAL300000078727
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078727'
/scratch/stefan/7769659/working/building/REAL300000078727 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078727

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078727/0 /scratch/stefan/7769659/working/building/REAL300000078727 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/724
`/scratch/stefan/7769659/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=N2)C1)

`REAL300000078727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078727 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 11, 21, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 29, 52, 52, 52, 29, 52, 52, 52, 1, 11, 11, 11, 1, 1, 7, 29, 52, 29, 52, 11, 11] 117
rigid atoms, others: [6, 8, 9, 10, 11, 12, 23, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078727 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 90, 117, 117, 117, 91, 117, 117, 117, 11, 1, 1, 1, 11, 11, 29, 90, 117, 102, 117, 1, 1] 117
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 367
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078727 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC(Cl)=CC(Cl)=C3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 65, 162, 65, 65, 65, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 162, 162, 162, 65, 65, 36, 9, 1, 1, 1, 162, 162] 162
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 379
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078727 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078727
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078727/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078727
Building REAL300000078728
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078728'
/scratch/stefan/7769659/working/building/REAL300000078728 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078728

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078728/0 /scratch/stefan/7769659/working/building/REAL300000078728 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/725
`/scratch/stefan/7769659/working/3D/725' -> `0.mol2'
Preparing input files

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

`REAL300000078728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078728 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 35, 35, 35, 35, 21, 21, 1, 1, 1, 35, 35] 35
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078728 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 26, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 8, 8, 35, 35, 35, 1, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078728 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078728
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078728/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078728
Building REAL300000078729
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078729'
/scratch/stefan/7769659/working/building/REAL300000078729 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078729

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078729/0 /scratch/stefan/7769659/working/building/REAL300000078729 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/726
`/scratch/stefan/7769659/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078729 none O=C([O-])COC1=CC=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 58, 58, 58, 58, 58, 58, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 201, 201, 58, 58, 58, 58, 22, 22, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 588
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078729 none O=C([O-])COC1=CC=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 30, 62, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 39, 39, 58, 58, 58, 58, 58, 58, 58, 58, 58, 31, 31, 1, 1, 1, 1, 8, 8, 58, 58, 58] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078729 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078729
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078729/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078729
Building REAL300000078730
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078730'
/scratch/stefan/7769659/working/building/REAL300000078730 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078730

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078730/0 /scratch/stefan/7769659/working/building/REAL300000078730 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/727
`/scratch/stefan/7769659/working/3D/727' -> `0.mol2'
Preparing input files

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

`REAL300000078730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078730 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 7, 35, 35, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 12, 12, 12, 13, 12, 13, 12, 1, 1, 7, 7, 7, 7, 62, 62, 62, 1, 1, 13, 13, 1, 1] 143
rigid atoms, others: [1, 35, 36, 39, 40, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078730 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 62, 62, 32, 44, 143, 143, 143, 143, 143, 143, 143, 62, 62, 27, 27, 27, 27, 1, 1, 1, 62, 62, 143, 143, 62, 62] 143
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 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])
total number of confs: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078730 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [48, 5, 48, 124, 124, 143, 143, 142, 143, 143, 143, 143, 143, 143, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 48, 48, 48, 48, 143, 143, 142, 13, 13, 1, 1, 13, 13] 143
rigid atoms, others: [37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 320
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078730 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078730
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078730/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078730
Building REAL300000078731
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078731'
/scratch/stefan/7769659/working/building/REAL300000078731 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078731

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078731/0 /scratch/stefan/7769659/working/building/REAL300000078731 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/728
`/scratch/stefan/7769659/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-])

`REAL300000078731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078731 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 34, 34, 34, 34, 119, 199, 201, 201, 69, 69, 69, 34, 7, 7, 1, 1, 1, 34, 34, 199, 199] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 661
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078731 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 35, 35, 1, 1, 1, 1, 9, 20, 35, 35, 3, 3, 3, 1, 6, 6, 34, 34, 34, 1, 1, 20, 20] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 18, 19, 20, 21, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078731 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078731
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078731/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078731
Building REAL300000078732
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078732'
/scratch/stefan/7769659/working/building/REAL300000078732 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078732

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078732/0 /scratch/stefan/7769659/working/building/REAL300000078732 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/729
`/scratch/stefan/7769659/working/3D/729' -> `0.mol2'
Preparing input files

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

`REAL300000078732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078732 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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
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, 113, 48, 22, 67, 67, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 67, 67, 201, 201, 67, 67, 22, 22, 1, 1, 1, 67, 67] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 783
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078732 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 11, 19, 3, 1, 1, 1, 1, 1, 1, 8, 51, 51, 67, 67, 67, 67, 67, 67, 67, 68, 68, 1, 1, 11, 11, 1, 1, 8, 8, 67, 67, 67, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 165
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078732 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078732
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078732/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078732
Building REAL300000078733
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078733'
/scratch/stefan/7769659/working/building/REAL300000078733 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078733

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078733/0 /scratch/stefan/7769659/working/building/REAL300000078733 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/730
`/scratch/stefan/7769659/working/3D/730' -> `0.mol2'
Preparing input files

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

`REAL300000078733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078733 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 40, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 7, 23, 36, 36, 1, 9, 9, 9, 9, 55, 55, 55, 1, 1, 1, 23, 23, 1] 201
rigid atoms, others: [32, 1, 34, 37, 33, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 205
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078733 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 55, 55, 55, 55, 55, 139, 201, 201, 201, 55, 15, 15, 15, 15, 1, 1, 1, 55, 55, 55, 201, 201, 55] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 548
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078733 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078733
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078733/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078733
Building REAL300000078734
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078734'
/scratch/stefan/7769659/working/building/REAL300000078734 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078734

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078734/0 /scratch/stefan/7769659/working/building/REAL300000078734 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/731
`/scratch/stefan/7769659/working/3D/731' -> `0.mol2'
Preparing input files

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

`REAL300000078734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078734 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 27, 27, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 29, 29, 29, 1, 1, 1, 1] 29
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078734 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 18, 29, 29, 18, 29, 29, 29, 29, 29, 18, 18, 18, 18, 1, 1, 1, 29, 29, 29, 29] 29
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078734 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078734
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078734/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078734
Building REAL300000078735
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078735'
/scratch/stefan/7769659/working/building/REAL300000078735 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078735

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078735/0 /scratch/stefan/7769659/working/building/REAL300000078735 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/732
`/scratch/stefan/7769659/working/3D/732' -> `0.mol2'
Preparing input files

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

`REAL300000078735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078735 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 33, 33, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 7, 44, 44, 44, 1, 1, 2, 2, 1, 1] 60
rigid atoms, others: [32, 1, 35, 36, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078735 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 20, 44, 44, 20, 20, 60, 60, 60, 44, 44, 20, 20, 20, 20, 1, 1, 1, 44, 44, 60, 60, 44, 44] 60
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 310
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078735 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078735
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078735/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078735
Building REAL300000078736
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078736'
/scratch/stefan/7769659/working/building/REAL300000078736 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078736

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078736/0 /scratch/stefan/7769659/working/building/REAL300000078736 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/733
`/scratch/stefan/7769659/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)

`REAL300000078736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078736 none O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 197, 137, 45, 15, 70, 70, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 70, 70, 201, 201, 197, 197, 70, 70, 15, 15, 1, 1, 1, 70, 70] 201
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 708
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078736 none O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 17, 11, 3, 1, 1, 1, 1, 1, 1, 8, 60, 60, 70, 70, 70, 70, 70, 70, 70, 71, 71, 1, 1, 13, 13, 11, 11, 1, 1, 8, 8, 70, 70, 70, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 23, 24, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 172
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078736 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078736
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078736/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078736
Building REAL300000078737
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078737'
/scratch/stefan/7769659/working/building/REAL300000078737 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078737

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078737/0 /scratch/stefan/7769659/working/building/REAL300000078737 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/734
`/scratch/stefan/7769659/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1)C(=O)[O-])

`REAL300000078737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078737 none CC(OC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 166, 49, 49, 48, 49, 49, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 49, 201, 201, 201, 201, 201, 201, 201, 48, 49, 49, 15, 15, 1, 1, 1, 49] 201
rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 456
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078737 none CC(OC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 8, 44, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 24, 29, 29, 24, 24, 24, 24, 1, 1, 1, 8, 8, 49, 49, 49, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 37, 21, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 171
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078737 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078737
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078737/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078737
Building REAL300000078738
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078738'
/scratch/stefan/7769659/working/building/REAL300000078738 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078738

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078738/0 /scratch/stefan/7769659/working/building/REAL300000078738 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/735
`/scratch/stefan/7769659/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1)

`REAL300000078738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078738 none O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 201, 176, 36, 36, 36, 36, 36, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 36, 201, 201, 200, 200, 36, 36, 36, 11, 11, 1, 1, 1, 36] 201
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 375
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078738 none O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 10, 18, 10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 34, 35, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 10, 10, 10, 10, 1, 1, 1, 6, 6, 37, 37, 37, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36])
total number of confs: 123
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078738 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078738
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078738/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078738
Building REAL300000078739
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078739'
/scratch/stefan/7769659/working/building/REAL300000078739 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078739

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078739/0 /scratch/stefan/7769659/working/building/REAL300000078739 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/736
`/scratch/stefan/7769659/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1[N+](=O)[O-])

`REAL300000078739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078739 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 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, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 7, 7, 5, 5, 5, 3, 1, 1, 1, 5] 7
rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078739 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 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: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 5, 5, 1, 1, 2, 4, 5, 5, 5, 1] 7
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 36, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 32
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078739 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078739/1 /scratch/stefan/7769659/working/building/REAL300000078739 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/737
`/scratch/stefan/7769659/working/3D/737' -> `1.mol2'
Preparing input files

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

`REAL300000078739.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078739/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078739 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 177, 13, 13, 63, 63, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 63, 63, 63, 64, 64, 201, 201, 63, 63, 13, 13, 1, 1, 1, 63] 201
rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078739 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 21, 25, 7, 1, 1, 1, 1, 1, 1, 8, 52, 52, 63, 63, 63, 63, 63, 63, 63, 64, 64, 1, 1, 1, 2, 2, 21, 21, 1, 1, 8, 8, 63, 63, 63, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 36, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078739 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078739
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078739/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078739/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078739
Building REAL300000078740
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078740'
/scratch/stefan/7769659/working/building/REAL300000078740 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078740

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078740/0 /scratch/stefan/7769659/working/building/REAL300000078740 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/738
`/scratch/stefan/7769659/working/3D/738' -> `0.mol2'
Preparing input files

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

`REAL300000078740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078740 none O=C([O-])COC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 140, 48, 48, 48, 48, 48, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 48, 201, 201, 48, 48, 48, 18, 18, 1, 1, 1, 48] 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])
total number of confs: 568
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078740 none O=C([O-])COC1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 18, 29, 6, 1, 1, 1, 1, 1, 1, 1, 7, 38, 39, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 18, 18, 1, 1, 1, 7, 7, 49, 49, 49, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 23, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 171
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078740 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078740
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078740/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078740
Building REAL300000078741
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078741'
/scratch/stefan/7769659/working/building/REAL300000078741 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078741

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078741/0 /scratch/stefan/7769659/working/building/REAL300000078741 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/739
`/scratch/stefan/7769659/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)OC=C1)

`REAL300000078741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078741 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 10, 13, 9, 5, 1, 1, 1, 1, 1, 1, 1, 8, 66, 66, 105, 105, 105, 105, 105, 105, 105, 106, 106, 1, 1, 9, 9, 9, 5, 5, 1, 1, 8, 8, 105, 105, 105, 1, 1, 9, 9] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 38, 39, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 198
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078741 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 52, 170, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 5, 5, 9, 9, 52, 52, 201, 201, 201, 9, 9, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 40, 41, 26, 27, 28] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 396
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078741 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 127, 105, 104, 36, 105, 105, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 105, 105, 200, 200, 200, 128, 127, 105, 105, 28, 28, 1, 1, 1, 105, 105, 200, 201] 201
rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41])
total number of confs: 631
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078741 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078741
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078741/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078741
Building REAL300000078742
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078742'
/scratch/stefan/7769659/working/building/REAL300000078742 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078742

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078742/0 /scratch/stefan/7769659/working/building/REAL300000078742 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/740
`/scratch/stefan/7769659/working/3D/740' -> `0.mol2'
Preparing input files

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

`REAL300000078742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078742 none COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 53, 32, 54, 54, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 54, 54, 114, 199, 201, 201, 54, 72, 72, 72, 54, 54, 24, 24, 1, 1, 1, 199, 199, 54] 201
rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 717
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078742 none COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 35, 35, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 7, 30, 58, 58, 1, 3, 3, 3, 1, 1, 7, 7, 54, 54, 54, 30, 30, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 25, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 285
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078742 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078742
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078742/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078742
Building REAL300000078743
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078743'
/scratch/stefan/7769659/working/building/REAL300000078743 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078743

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078743/0 /scratch/stefan/7769659/working/building/REAL300000078743 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/741
`/scratch/stefan/7769659/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)

`REAL300000078743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078743 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [195, 195, 195, 109, 195, 195, 8, 8, 35, 35, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 35, 35, 35, 35, 8, 8, 1, 1, 1, 35, 35] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 652
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078743 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 22, 29, 6, 22, 22, 1, 1, 1, 1, 1, 1, 6, 34, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 6, 6, 36, 36, 36, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078743 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078743
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078743/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078743
Building REAL300000078744
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078744'
/scratch/stefan/7769659/working/building/REAL300000078744 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078744

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078744/0 /scratch/stefan/7769659/working/building/REAL300000078744 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/742
`/scratch/stefan/7769659/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078744 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 52, 52, 52, 51, 19, 19, 1, 1, 1] 52
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])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078744 none CN1C(C(=O)[O-])=CC(Br)=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 1, 1, 7, 37, 37, 51, 51, 51, 51, 51, 51, 51, 52, 52, 2, 2, 2, 1, 7, 7, 51, 51, 51] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078744 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078744
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078744/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078744
Building REAL300000078745
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078745'
/scratch/stefan/7769659/working/building/REAL300000078745 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078745

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078745/0 /scratch/stefan/7769659/working/building/REAL300000078745 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/743
`/scratch/stefan/7769659/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)

`REAL300000078745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078745 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 140, 140, 140, 140, 140, 140, 140, 140, 140, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 140, 140, 140, 140, 140, 140, 40, 40, 1, 1, 1, 140, 140] 140
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])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078745 none COC1=C2OC(C(=O)[O-])=CC2=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 66, 66, 140, 140, 140, 140, 140, 140, 140, 140, 140, 1, 1, 3, 3, 3, 1, 9, 9, 140, 140, 140, 1, 1] 140
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 37, 30, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078745 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078745/1 /scratch/stefan/7769659/working/building/REAL300000078745 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/744
`/scratch/stefan/7769659/working/3D/744' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)

`REAL300000078745.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078745/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078745 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 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
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, 42, 42, 42, 42, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 42, 42, 42, 42, 42, 42, 19, 5, 1, 1, 1, 42, 42] 42
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])
total number of confs: 68
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078745 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 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
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 12, 12, 34, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 4, 4, 4, 1, 12, 34, 42, 42, 42, 1, 1] 42
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 37, 30, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078745 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078745
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078745/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078745/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078745
Building REAL300000078746
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078746'
/scratch/stefan/7769659/working/building/REAL300000078746 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078746

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078746/0 /scratch/stefan/7769659/working/building/REAL300000078746 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/745
`/scratch/stefan/7769659/working/3D/745' -> `0.mol2'
Preparing input files

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

`REAL300000078746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078746 none CCC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [11, 7, 1, 7, 30, 30, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 7, 42, 42, 42, 1, 1, 1, 1] 42
rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078746 none CCC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [27, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 42, 42, 26, 24, 42, 42, 42, 42, 33, 33, 33, 33, 33, 23, 1, 1, 1, 42, 42, 42, 42] 42
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078746 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078746
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078746/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078746
Building REAL300000078747
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078747'
/scratch/stefan/7769659/working/building/REAL300000078747 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078747

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078747/0 /scratch/stefan/7769659/working/building/REAL300000078747 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/746
`/scratch/stefan/7769659/working/3D/746' -> `0.mol2'
Preparing input files

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

`REAL300000078747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078747 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 36, 36, 36, 1, 1, 1, 1] 36
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078747 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 36, 36, 33, 36, 36, 36, 36, 36, 27, 27, 27, 27, 1, 1, 1, 36, 36, 36, 36] 36
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078747 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078747
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078747/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078747
Building REAL300000078748
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078748'
/scratch/stefan/7769659/working/building/REAL300000078748 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078748

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078748/0 /scratch/stefan/7769659/working/building/REAL300000078748 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/747
`/scratch/stefan/7769659/working/3D/747' -> `0.mol2'
Preparing input files

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

`REAL300000078748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078748 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 31, 31, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 34, 34, 34, 1, 1, 1, 2] 68
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 67
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078748 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 1, 1, 1, 34, 34, 34, 68] 68
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 161
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078748 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078748
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078748/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078748
Building REAL300000078749
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078749'
/scratch/stefan/7769659/working/building/REAL300000078749 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078749

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078749/0 /scratch/stefan/7769659/working/building/REAL300000078749 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/748
`/scratch/stefan/7769659/working/3D/748' -> `0.mol2'
Preparing input files

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

`REAL300000078749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078749 none CCC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [16, 10, 1, 10, 41, 41, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 19, 19, 19, 19, 19, 10, 71, 71, 71, 1, 1, 1] 71
rigid atoms, others: [2, 35, 36, 34, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078749 none CCC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [33, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 71, 71, 71, 71, 71, 71, 71, 71, 71, 39, 39, 39, 39, 39, 25, 1, 1, 1, 71, 71, 71] 71
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078749 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078749
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078749/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078749
Building REAL300000078750
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078750'
/scratch/stefan/7769659/working/building/REAL300000078750 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078750

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078750/0 /scratch/stefan/7769659/working/building/REAL300000078750 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/749
`/scratch/stefan/7769659/working/3D/749' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=NNC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=C2C=C1)

`REAL300000078750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078750 none O=C([O-])C1=CC2=NNC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 80, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 80, 80, 80, 80, 80, 33, 33, 1, 1, 1, 80, 80] 80
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078750 none O=C([O-])C1=CC2=NNC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=C2C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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
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, 1, 1, 9, 56, 56, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 9, 9, 80, 80, 80, 1, 1] 80
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078750 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078750
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078750/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078750
Building REAL300000078751
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078751'
/scratch/stefan/7769659/working/building/REAL300000078751 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078751

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078751/0 /scratch/stefan/7769659/working/building/REAL300000078751 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/750
`/scratch/stefan/7769659/working/3D/750' -> `0.mol2'
Preparing input files

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

`REAL300000078751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078751 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 49, 49, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 54, 54, 54, 1, 1, 1, 1] 54
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078751 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 54, 54, 54, 54, 54, 54, 54, 54, 25, 25, 25, 25, 1, 1, 1, 54, 54, 54, 54] 54
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078751 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078751
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078751/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078751
Building REAL300000078752
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078752'
/scratch/stefan/7769659/working/building/REAL300000078752 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078752

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078752/0 /scratch/stefan/7769659/working/building/REAL300000078752 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/751
`/scratch/stefan/7769659/working/3D/751' -> `0.mol2'
Preparing input files

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

`REAL300000078752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078752 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 135, 135, 135, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 135, 135, 201, 201, 135, 35, 35, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 601
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078752 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])N=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 18, 1, 1, 1, 1, 1, 9, 67, 67, 135, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 8, 8, 1, 9, 9, 135, 135, 135] 201
rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078752 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078752
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078752/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078752
Building REAL300000078753
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078753'
/scratch/stefan/7769659/working/building/REAL300000078753 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078753

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078753/0 /scratch/stefan/7769659/working/building/REAL300000078753 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/752
`/scratch/stefan/7769659/working/3D/752' -> `0.mol2'
Preparing input files

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

`REAL300000078753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078753 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 59, 59, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 13, 76, 76, 76, 1, 1, 1] 76
rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078753 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 76, 76, 76, 76, 76, 76, 76, 76, 76, 24, 24, 24, 24, 1, 1, 1, 76, 76, 76] 76
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078753 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078753
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078753/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078753
Building REAL300000078754
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078754'
/scratch/stefan/7769659/working/building/REAL300000078754 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078754

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078754/0 /scratch/stefan/7769659/working/building/REAL300000078754 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/753
`/scratch/stefan/7769659/working/3D/753' -> `0.mol2'
Preparing input files

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

`REAL300000078754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078754 none O=C([O-])C1=CSC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 84, 84, 23, 23, 1, 1, 1, 84] 84
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078754 none O=C([O-])C1=CSC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 9, 50, 50, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 9, 9, 84, 84, 84, 1] 84
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078754 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078754
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078754/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078754
Building REAL300000078755
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078755'
/scratch/stefan/7769659/working/building/REAL300000078755 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078755

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078755/0 /scratch/stefan/7769659/working/building/REAL300000078755 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/754
`/scratch/stefan/7769659/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCCC(=O)[O-])

`REAL300000078755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078755 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 34, 34, 34, 34, 118, 184, 184, 201, 195, 69, 69, 69, 34, 7, 7, 1, 1, 1, 34, 34, 184, 184, 184, 184] 201
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 645
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078755 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 35, 35, 1, 1, 1, 1, 7, 11, 11, 25, 23, 3, 3, 3, 1, 6, 6, 34, 34, 34, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078755 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078755
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078755/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078755
Building REAL300000078756
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078756'
/scratch/stefan/7769659/working/building/REAL300000078756 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078756

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078756/0 /scratch/stefan/7769659/working/building/REAL300000078756 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/755
`/scratch/stefan/7769659/working/3D/755' -> `0.mol2'
Preparing input files

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

`REAL300000078756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078756 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 33, 62, 17, 62, 62, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 62, 62, 62, 62, 62, 17, 17, 1, 1, 1, 62] 62
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 308
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078756 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 8, 48, 48, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 8, 8, 62, 62, 62, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078756 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078756
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078756/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078756
Building REAL300000078757
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078757'
/scratch/stefan/7769659/working/building/REAL300000078757 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078757

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078757/0 /scratch/stefan/7769659/working/building/REAL300000078757 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/756
`/scratch/stefan/7769659/working/3D/756' -> `0.mol2'
Preparing input files

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

`REAL300000078757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078757 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 5, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 26, 26, 26, 26, 26, 26, 26, 20, 20, 20, 20, 1, 1, 1] 26
rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078757 none CC1=NC(C)=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 2, 2, 1, 1, 1, 5, 5, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 26, 26, 26] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078757 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078757
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078757/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078757
Building REAL300000078758
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078758'
/scratch/stefan/7769659/working/building/REAL300000078758 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078758

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078758/0 /scratch/stefan/7769659/working/building/REAL300000078758 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/757
`/scratch/stefan/7769659/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O)

`REAL300000078758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078758 none O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [20, 19, 20, 19, 19, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 19, 19, 19, 19, 19, 12, 5, 1, 1, 1, 19, 19, 38] 40
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078758 none O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 15, 19, 19, 19, 19, 19, 19, 19, 20, 20, 1, 1, 1, 1, 1, 6, 15, 19, 19, 19, 1, 1, 2] 40
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 31])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078758 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078758/1 /scratch/stefan/7769659/working/building/REAL300000078758 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/758
`/scratch/stefan/7769659/working/3D/758' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O)

`REAL300000078758.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078758/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078758 none O=C([O-])C1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
230  conformations in input
total number of sets (complete confs): 230
using faster count positions algorithm for large data
unique positions, atoms: [115, 114, 115, 114, 114, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 114, 114, 114, 114, 114, 34, 34, 1, 1, 1, 114, 114, 228] 230
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 447
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078758 none O=C([O-])C1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
230  conformations in input
total number of sets (complete confs): 230
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 67, 67, 114, 114, 114, 114, 114, 114, 114, 115, 115, 1, 1, 1, 1, 1, 8, 8, 114, 114, 114, 1, 1, 2] 230
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 31])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078758 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078758
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078758/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078758/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078758
Building REAL300000078759
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078759'
/scratch/stefan/7769659/working/building/REAL300000078759 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078759

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078759/0 /scratch/stefan/7769659/working/building/REAL300000078759 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/759
`/scratch/stefan/7769659/working/3D/759' -> `0.mol2'
Preparing input files

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

`REAL300000078759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078759 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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
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, 20, 5, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 24, 24, 24, 24, 24, 20, 20, 20, 20, 1, 1, 1] 24
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 71
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078759 none CC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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
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, 2, 2, 1, 1, 1, 5, 5, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 24, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 27, 28, 29] set([6, 7, 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: 52
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078759 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078759
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078759/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078759
Building REAL300000078760
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078760'
/scratch/stefan/7769659/working/building/REAL300000078760 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078760

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078760/0 /scratch/stefan/7769659/working/building/REAL300000078760 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/760
`/scratch/stefan/7769659/working/3D/760' -> `0.mol2'
Preparing input files

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

`REAL300000078760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078760 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 51, 51, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 58, 58, 58, 1, 1] 58
rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078760 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 22, 58, 58, 58, 58, 58, 58, 58, 22, 22, 22, 22, 1, 1, 1, 58, 58] 58
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078760 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078760
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078760/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078760
Building REAL300000078761
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078761'
/scratch/stefan/7769659/working/building/REAL300000078761 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078761

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078761/0 /scratch/stefan/7769659/working/building/REAL300000078761 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/761
`/scratch/stefan/7769659/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)C(=O)[O-])

`REAL300000078761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078761 none CC(OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 160, 57, 21, 76, 76, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 76, 76, 201, 201, 201, 201, 201, 201, 201, 76, 76, 21, 21, 1, 1, 1, 76, 76] 201
rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 656
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078761 none CC(OC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 8, 54, 54, 76, 76, 76, 76, 76, 76, 76, 77, 77, 1, 1, 16, 23, 23, 16, 16, 16, 16, 1, 1, 8, 8, 76, 76, 76, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 36, 29, 30, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 204
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078761 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078761
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078761/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078761
Building REAL300000078762
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078762'
/scratch/stefan/7769659/working/building/REAL300000078762 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078762

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078762/0 /scratch/stefan/7769659/working/building/REAL300000078762 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/762
`/scratch/stefan/7769659/working/3D/762' -> `0.mol2'
Preparing input files

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

`REAL300000078762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078762 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 95, 95, 95, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 95, 95, 95, 95, 95, 95, 201, 201, 95, 24, 24, 1, 1, 1, 95, 95, 95, 95] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 656
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078762 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 14, 1, 1, 1, 1, 1, 8, 55, 56, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 95, 95, 95, 1, 1, 1, 1] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 24, 25, 28, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078762 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078762
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078762/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078762
Building REAL300000078763
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078763'
/scratch/stefan/7769659/working/building/REAL300000078763 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078763

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078763/0 /scratch/stefan/7769659/working/building/REAL300000078763 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/763
`/scratch/stefan/7769659/working/3D/763' -> `0.mol2'
Preparing input files

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

`REAL300000078763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078763 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 137, 137, 137, 137, 137, 35, 35, 1, 1, 1, 137] 137
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 238
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078763 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 73, 73, 137, 137, 137, 137, 137, 137, 137, 137, 137, 1, 2, 2, 2, 1, 9, 9, 137, 137, 137, 1] 137
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078763 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078763
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078763/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078763
Building REAL300000078764
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078764'
/scratch/stefan/7769659/working/building/REAL300000078764 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078764

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078764/0 /scratch/stefan/7769659/working/building/REAL300000078764 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/764
`/scratch/stefan/7769659/working/3D/764' -> `0.mol2'
Preparing input files

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

`REAL300000078764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078764 none O=C([O-])C1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 76, 76, 76, 76, 31, 31, 1, 1, 1, 76] 76
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078764 none O=C([O-])C1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 51, 51, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 8, 8, 76, 76, 76, 1] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078764 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078764/1 /scratch/stefan/7769659/working/building/REAL300000078764 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/765
`/scratch/stefan/7769659/working/3D/765' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1)

`REAL300000078764.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078764/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078764 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 14, 15, 15, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 14, 15, 15, 11, 5, 1, 1, 1, 15] 15
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078764 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 7, 7, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 13, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078764 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078764
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078764/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078764/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078764
Building REAL300000078765
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078765'
/scratch/stefan/7769659/working/building/REAL300000078765 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078765

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078765/0 /scratch/stefan/7769659/working/building/REAL300000078765 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/766
`/scratch/stefan/7769659/working/3D/766' -> `0.mol2'
Preparing input files

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

`REAL300000078765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078765 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 20, 28, 50, 72, 72, 1, 5, 5, 5, 5, 25, 25, 25, 1, 1, 1, 20, 20, 28, 28, 50, 50, 1] 201
rigid atoms, others: [1, 34, 35, 36, 43, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 351
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078765 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 25, 25, 25, 25, 25, 87, 144, 153, 201, 201, 201, 25, 11, 11, 11, 11, 1, 1, 1, 25, 25, 25, 144, 144, 153, 153, 201, 201, 25] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 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, 43])
total number of confs: 722
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078765 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078765
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078765/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078765
Building REAL300000078766
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078766'
/scratch/stefan/7769659/working/building/REAL300000078766 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078766

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078766/0 /scratch/stefan/7769659/working/building/REAL300000078766 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/767
`/scratch/stefan/7769659/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078766 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [16, 3, 16, 47, 54, 57, 57, 55, 57, 169, 201, 201, 201, 201, 57, 57, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 51, 51, 54, 54, 57, 57, 201, 201, 201, 201, 57, 57, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 585
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078766 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 4, 1, 1, 1, 1, 1, 1, 11, 25, 25, 31, 31, 1, 1, 12, 48, 48, 57, 57, 57, 57, 57, 57, 57, 57, 57, 12, 12, 12, 12, 6, 6, 4, 4, 1, 1, 25, 25, 25, 25, 1, 1, 57, 57, 57] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46])
total number of confs: 202
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078766 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078766
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078766/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078766
Building REAL300000078767
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078767'
/scratch/stefan/7769659/working/building/REAL300000078767 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078767

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078767/0 /scratch/stefan/7769659/working/building/REAL300000078767 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/768
`/scratch/stefan/7769659/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078767 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 3, 19, 45, 52, 57, 57, 52, 57, 133, 201, 201, 201, 57, 57, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 19, 19, 19, 19, 49, 49, 52, 52, 57, 57, 201, 201, 57, 57, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 721
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078767 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 4, 1, 1, 1, 1, 1, 1, 6, 20, 30, 30, 1, 1, 12, 44, 44, 57, 57, 57, 57, 57, 57, 57, 57, 57, 12, 12, 12, 12, 6, 6, 4, 4, 1, 1, 21, 21, 1, 1, 57, 57, 57] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 39, 13, 14, 40, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43])
total number of confs: 207
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078767 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078767
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078767/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078767
Building REAL300000078768
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078768'
/scratch/stefan/7769659/working/building/REAL300000078768 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078768

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078768/0 /scratch/stefan/7769659/working/building/REAL300000078768 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/769
`/scratch/stefan/7769659/working/3D/769' -> `0.mol2'
Preparing input files

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

`REAL300000078768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078768 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 36, 36, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 10, 24, 24, 35, 35, 1, 8, 8, 8, 8, 48, 48, 48, 1, 1, 1, 24, 24, 24, 24, 1] 201
rigid atoms, others: [1, 34, 35, 33, 40, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 196
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078768 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 48, 48, 48, 48, 48, 154, 201, 201, 201, 201, 48, 17, 17, 17, 17, 1, 1, 1, 48, 48, 48, 201, 201, 201, 201, 48] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 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])
total number of confs: 516
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078768 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078768
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078768/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078768
Building REAL300000078769
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078769'
/scratch/stefan/7769659/working/building/REAL300000078769 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078769

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078769/0 /scratch/stefan/7769659/working/building/REAL300000078769 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/770
`/scratch/stefan/7769659/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078769 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 3, 22, 44, 49, 55, 55, 49, 55, 182, 200, 201, 201, 201, 55, 55, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 22, 22, 22, 22, 45, 45, 49, 49, 55, 55, 200, 200, 201, 201, 55, 55, 1, 1, 1] 201
rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 508
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078769 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 4, 1, 1, 1, 1, 1, 1, 6, 18, 20, 26, 26, 1, 1, 11, 40, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 11, 11, 11, 11, 6, 6, 4, 4, 1, 1, 18, 19, 19, 19, 1, 1, 55, 55, 55] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46])
total number of confs: 193
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078769 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078769
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078769/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078769
Building REAL300000078770
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078770'
/scratch/stefan/7769659/working/building/REAL300000078770 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078770

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078770/0 /scratch/stefan/7769659/working/building/REAL300000078770 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/771
`/scratch/stefan/7769659/working/3D/771' -> `0.mol2'
Preparing input files

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

`REAL300000078770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078770 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 48, 48, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 56, 56, 56, 1, 1] 56
rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078770 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 26, 56, 56, 56, 56, 56, 56, 56, 26, 26, 26, 26, 1, 1, 1, 56, 56] 56
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078770 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078770/1 /scratch/stefan/7769659/working/building/REAL300000078770 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/772
`/scratch/stefan/7769659/working/3D/772' -> `1.mol2'
Preparing input files

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

`REAL300000078770.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078770/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078770 none CC(=NNC1=CC=CC(F)=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [12, 1, 12, 12, 35, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 35, 37, 37, 37, 1, 1] 37
rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078770 none CC(=NNC1=CC=CC(F)=C1[N+](=O)[O-])C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 37, 37, 37, 37, 37, 37, 37, 16, 16, 16, 5, 1, 1, 1, 37, 37] 37
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 65
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078770 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078770
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078770/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078770/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078770
Building REAL300000078771
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078771'
/scratch/stefan/7769659/working/building/REAL300000078771 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078771

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078771/0 /scratch/stefan/7769659/working/building/REAL300000078771 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/773
`/scratch/stefan/7769659/working/3D/773' -> `0.mol2'
Preparing input files

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

`REAL300000078771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078771 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4] 15
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 29
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078771 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [3, 1, 3, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 4, 2, 4, 4, 1, 1, 1, 13, 13, 13, 1, 1] 15
rigid atoms, others: [32, 1, 3, 4, 37, 10, 11, 12, 24, 36, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 35
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078771 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [14, 13, 14, 13, 13, 15, 15, 14, 15, 15, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 15, 15, 15, 15, 15, 13, 13, 13, 1, 1, 1, 13, 13] 15
rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 45
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078771 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078771
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078771/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078771
Building REAL300000078772
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078772'
/scratch/stefan/7769659/working/building/REAL300000078772 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078772

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078772/0 /scratch/stefan/7769659/working/building/REAL300000078772 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/774
`/scratch/stefan/7769659/working/3D/774' -> `0.mol2'
Preparing input files

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

`REAL300000078772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078772 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 29, 29, 29, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 42
rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078772 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 29, 29, 29, 29, 29, 42, 42, 42, 29, 29, 29, 23, 23, 23, 23, 1, 1, 1, 29, 29, 42, 42, 29, 29, 29, 29, 29, 29] 42
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078772 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078772
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078772/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078772
Building REAL300000078773
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078773'
/scratch/stefan/7769659/working/building/REAL300000078773 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078773

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078773/0 /scratch/stefan/7769659/working/building/REAL300000078773 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/775
`/scratch/stefan/7769659/working/3D/775' -> `0.mol2'
Preparing input files

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

`REAL300000078773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078773 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 4, 23, 54, 68, 84, 120, 131, 199, 201, 201, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 23, 23, 23, 57, 57, 65, 68, 90, 90, 118, 122, 137, 137, 198, 200, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1022
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078773 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078773
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078773/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078773
Building REAL300000078774
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078774'
/scratch/stefan/7769659/working/building/REAL300000078774 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078774

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078774/0 /scratch/stefan/7769659/working/building/REAL300000078774 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/776
`/scratch/stefan/7769659/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078774 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 37, 37, 37, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 24, 24, 24, 24, 37, 37, 24, 24, 24, 24, 24, 1, 1, 1] 37
rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078774 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 10, 14, 14, 1, 1, 1, 1, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 10, 10, 1, 1, 1, 1, 1, 24, 24, 24] 37
rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 25, 26, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078774 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078774
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078774/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078774
Building REAL300000078775
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078775'
/scratch/stefan/7769659/working/building/REAL300000078775 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078775

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078775/0 /scratch/stefan/7769659/working/building/REAL300000078775 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/777
`/scratch/stefan/7769659/working/3D/777' -> `0.mol2'
Preparing input files

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

`REAL300000078775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078775 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [13, 1, 13, 50, 50, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 58, 58, 58, 1, 1] 58
rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078775 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 58, 58, 58, 58, 58, 58, 58, 24, 24, 24, 24, 1, 1, 1, 58, 58] 58
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078775 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078775
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078775/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078775
Building REAL300000078776
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078776'
/scratch/stefan/7769659/working/building/REAL300000078776 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078776

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078776/0 /scratch/stefan/7769659/working/building/REAL300000078776 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/778
`/scratch/stefan/7769659/working/3D/778' -> `0.mol2'
Preparing input files

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

`REAL300000078776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078776 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [14, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 1, 11, 11, 11, 36, 36, 36, 11, 11] 36
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 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: 73
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078776 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 11, 11, 11, 11, 11, 11, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 11, 11, 11, 11, 1, 1, 1, 16, 16, 16, 1, 1] 36
rigid atoms, others: [32, 1, 3, 4, 37, 11, 12, 13, 25, 36, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 38
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078776 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=C2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [19, 16, 19, 16, 16, 36, 36, 36, 36, 36, 36, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 36, 36, 36, 36, 16, 16, 16, 1, 1, 1, 16, 16] 36
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])
total number of confs: 87
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078776 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078776
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078776/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078776
Building REAL300000078777
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078777'
/scratch/stefan/7769659/working/building/REAL300000078777 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078777

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078777/0 /scratch/stefan/7769659/working/building/REAL300000078777 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/779
`/scratch/stefan/7769659/working/3D/779' -> `0.mol2'
Preparing input files

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

`REAL300000078777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078777 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11
rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078777 none O=C([O-])C1=CC=C2C(=C1)CCCC2N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 15
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078777 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078777
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078777/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078777
Building REAL300000078778
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078778'
/scratch/stefan/7769659/working/building/REAL300000078778 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078778

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078778/0 /scratch/stefan/7769659/working/building/REAL300000078778 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/780
`/scratch/stefan/7769659/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078778 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [18, 4, 18, 23, 35, 35, 35, 35, 35, 35, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 18, 18, 18, 18, 23, 23, 35, 35, 35, 35, 35, 35, 1, 1, 1] 35
rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078778 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 6, 1, 1, 1, 3, 3, 1, 1, 1, 9, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35] 35
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078778 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078778
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078778/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078778
Building REAL300000078779
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078779'
/scratch/stefan/7769659/working/building/REAL300000078779 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078779

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078779/0 /scratch/stefan/7769659/working/building/REAL300000078779 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/781
`/scratch/stefan/7769659/working/3D/781' -> `0.mol2'
Preparing input files

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

`REAL300000078779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078779 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-])=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [71, 71, 71, 71, 71, 71, 71, 71, 31, 5, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 71, 71, 96, 96, 96, 71, 71, 71, 71, 71, 71, 31, 31, 31, 31, 1, 1, 1, 96, 96] 96
rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42])
total number of confs: 313
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078779 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-])=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 6, 6, 44, 44, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6, 71, 71, 71, 3, 3] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 23, 24, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078779 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078779
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078779/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078779
Building REAL300000078780
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078780'
/scratch/stefan/7769659/working/building/REAL300000078780 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078780

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078780/0 /scratch/stefan/7769659/working/building/REAL300000078780 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/782
`/scratch/stefan/7769659/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078780 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 47, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 1, 1, 1] 48
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078780 none CC1=CC(C)=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 48, 48, 48] 48
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078780 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078780/1 /scratch/stefan/7769659/working/building/REAL300000078780 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/783
`/scratch/stefan/7769659/working/3D/783' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078780.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078780/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078780 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 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
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, 23, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 19, 5, 1, 1, 1] 23
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078780 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 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
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, 2, 2, 1, 1, 1, 9, 9, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 2, 2, 2, 1, 9, 21, 23, 23, 23] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078780 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078780
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078780/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078780/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078780
Building REAL300000078781
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078781'
/scratch/stefan/7769659/working/building/REAL300000078781 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078781

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078781/0 /scratch/stefan/7769659/working/building/REAL300000078781 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/784
`/scratch/stefan/7769659/working/3D/784' -> `0.mol2'
Preparing input files

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

`REAL300000078781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078781 none O=C([O-])C1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 79, 79, 79, 79, 79, 30, 30, 1, 1, 1] 79
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078781 none O=C([O-])C1=CC=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 53, 54, 79, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 8, 8, 79, 79, 79] 79
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078781 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078781/1 /scratch/stefan/7769659/working/building/REAL300000078781 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/785
`/scratch/stefan/7769659/working/3D/785' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1Cl)

`REAL300000078781.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078781/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078781 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 18, 18, 18, 18, 18, 13, 5, 1, 1, 1] 18
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078781 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 8, 16, 18, 18, 18] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078781 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078781
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078781/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078781/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078781
Building REAL300000078782
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078782'
/scratch/stefan/7769659/working/building/REAL300000078782 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078782

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078782/0 /scratch/stefan/7769659/working/building/REAL300000078782 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/786
`/scratch/stefan/7769659/working/3D/786' -> `0.mol2'
Preparing input files

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

`REAL300000078782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078782 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078782 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 11
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078782 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078782
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078782/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078782
Building REAL300000078783
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078783'
/scratch/stefan/7769659/working/building/REAL300000078783 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078783

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078783/0 /scratch/stefan/7769659/working/building/REAL300000078783 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/787
`/scratch/stefan/7769659/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078783 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 54, 54, 54, 54, 27, 27, 1, 1, 1] 54
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078783 none CN1N=CC(C(=O)[O-])=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 3, 1, 1, 8, 39, 40, 54, 54, 54, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 8, 8, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 25] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 106
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078783 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078783
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078783/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078783
Building REAL300000078784
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078784'
/scratch/stefan/7769659/working/building/REAL300000078784 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078784

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078784/0 /scratch/stefan/7769659/working/building/REAL300000078784 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/788
`/scratch/stefan/7769659/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F)

`REAL300000078784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078784 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [122, 121, 122, 121, 121, 121, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 121, 121, 121, 121, 121, 23, 23, 1, 1, 1, 121] 122
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078784 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 8, 67, 67, 121, 121, 121, 121, 121, 121, 121, 122, 122, 1, 1, 1, 1, 1, 8, 8, 121, 121, 121, 1] 122
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078784 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078784/1 /scratch/stefan/7769659/working/building/REAL300000078784 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/789
`/scratch/stefan/7769659/working/3D/789' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F)

`REAL300000078784.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078784/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078784 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 36, 37, 36, 36, 36, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 36, 36, 36, 36, 36, 17, 5, 1, 1, 1, 36] 37
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078784 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1F NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 18, 36, 36, 36, 36, 36, 36, 36, 37, 37, 1, 1, 1, 1, 1, 6, 18, 36, 36, 36, 1] 37
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078784 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078784
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078784/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078784/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078784
Building REAL300000078785
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078785'
/scratch/stefan/7769659/working/building/REAL300000078785 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078785

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078785/0 /scratch/stefan/7769659/working/building/REAL300000078785 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/790
`/scratch/stefan/7769659/working/3D/790' -> `0.mol2'
Preparing input files

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

`REAL300000078785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078785 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [200, 201, 201, 201, 88, 88, 88, 88, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 88, 201, 201, 88, 88, 28, 28, 1, 1, 1] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 524
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078785 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 22, 11, 1, 1, 1, 1, 1, 1, 8, 60, 60, 88, 88, 88, 88, 88, 88, 88, 89, 89, 1, 11, 11, 1, 1, 8, 8, 88, 88, 88] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078785 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078785
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078785/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078785
Building REAL300000078786
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078786'
/scratch/stefan/7769659/working/building/REAL300000078786 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078786

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078786/0 /scratch/stefan/7769659/working/building/REAL300000078786 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/791
`/scratch/stefan/7769659/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078786 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 36, 42, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 3, 12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 42, 42, 42, 42, 42, 42, 42, 20, 20, 20, 12, 12, 12, 12, 1, 1, 1] 42
rigid atoms, others: [41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 121
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078786 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 20, 20, 20] 42
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 74
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078786 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078786
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078786/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078786
Building REAL300000078787
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078787'
/scratch/stefan/7769659/working/building/REAL300000078787 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078787

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078787/0 /scratch/stefan/7769659/working/building/REAL300000078787 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/792
`/scratch/stefan/7769659/working/3D/792' -> `0.mol2'
Preparing input files

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

`REAL300000078787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078787 none O=C([O-])C1=CC=CC2=C1C(N=NC1=CC=CC(F)=C1[N+](=O)[O-])CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15, 15, 15] 15
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078787 none O=C([O-])C1=CC=CC2=C1C(N=NC1=CC=CC(F)=C1[N+](=O)[O-])CC2 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 15, 15, 15, 1, 1, 1, 1] 15
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26, 27, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078787 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078787
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078787/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078787
Building REAL300000078788
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078788'
/scratch/stefan/7769659/working/building/REAL300000078788 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078788

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078788/0 /scratch/stefan/7769659/working/building/REAL300000078788 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/793
`/scratch/stefan/7769659/working/3D/793' -> `0.mol2'
Preparing input files

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

`REAL300000078788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078788 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 50, 50, 50, 1, 1, 3, 3] 71
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 24, 25, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078788 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
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, 3, 3, 1, 3, 10, 51, 51, 71, 71, 71, 71, 71, 71, 71, 71, 71, 3, 3, 1, 1, 1, 1, 3, 3, 10, 10, 71, 71, 71, 3, 3, 1, 1] 71
rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 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, 38])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078788 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 70, 71, 62, 71, 71, 49, 44, 49, 49, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 49, 49, 71, 71, 71, 71, 49, 49, 39, 39, 1, 1, 1, 49, 49, 71, 71] 71
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40])
total number of confs: 260
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078788 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078788
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078788/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078788
Building REAL300000078789
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078789'
/scratch/stefan/7769659/working/building/REAL300000078789 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078789

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078789/0 /scratch/stefan/7769659/working/building/REAL300000078789 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/794
`/scratch/stefan/7769659/working/3D/794' -> `0.mol2'
Preparing input files

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

`REAL300000078789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078789 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 53, 53, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 59, 59, 59, 1, 1, 1] 59
rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078789 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 59, 59, 59, 59, 59, 59, 59, 59, 27, 27, 27, 27, 1, 1, 1, 59, 59, 59] 59
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078789 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078789
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078789/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078789
Building REAL300000078790
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078790'
/scratch/stefan/7769659/working/building/REAL300000078790 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078790

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078790/0 /scratch/stefan/7769659/working/building/REAL300000078790 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/795
`/scratch/stefan/7769659/working/3D/795' -> `0.mol2'
Preparing input files

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

`REAL300000078790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078790 none O=C([O-])C1=CC=C2NC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
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, 68, 68, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 68, 68, 68, 68, 68, 68, 33, 33, 1, 1, 1, 68] 68
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078790 none O=C([O-])C1=CC=C2NC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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
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, 1, 1, 1, 9, 51, 51, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 9, 9, 68, 68, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 23, 24, 25, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078790 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078790
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078790/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078790
Building REAL300000078791
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078791'
/scratch/stefan/7769659/working/building/REAL300000078791 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078791

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078791/0 /scratch/stefan/7769659/working/building/REAL300000078791 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/796
`/scratch/stefan/7769659/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=N1)

`REAL300000078791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078791 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 72, 73, 72, 72, 72, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 72, 72, 72, 72, 27, 27, 1, 1, 1, 72] 73
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078791 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 40, 40, 72, 72, 72, 72, 72, 72, 72, 73, 73, 1, 1, 1, 1, 8, 8, 72, 72, 72, 1] 73
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078791 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078791/1 /scratch/stefan/7769659/working/building/REAL300000078791 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/797
`/scratch/stefan/7769659/working/3D/797' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=N1)

`REAL300000078791.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078791/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078791 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 18, 19, 18, 18, 18, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 18, 18, 18, 18, 9, 5, 1, 1, 1, 18] 19
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078791 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 14, 18, 18, 18, 18, 18, 18, 18, 19, 19, 1, 1, 1, 1, 6, 14, 18, 18, 18, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078791 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078791
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078791/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078791/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078791
Building REAL300000078792
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078792'
/scratch/stefan/7769659/working/building/REAL300000078792 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078792

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078792/0 /scratch/stefan/7769659/working/building/REAL300000078792 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/798
`/scratch/stefan/7769659/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1O)

`REAL300000078792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078792 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
214  conformations in input
total number of sets (complete confs): 214
using faster count positions algorithm for large data
unique positions, atoms: [107, 106, 107, 106, 107, 107, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 107, 107, 107, 107, 107, 22, 22, 1, 1, 1, 107, 214] 214
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 399
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078792 none O=C([O-])C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
214  conformations in input
total number of sets (complete confs): 214
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 68, 68, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 9, 9, 107, 107, 107, 1, 2] 214
rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078792 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078792
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078792/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078792
Building REAL300000078793
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078793'
/scratch/stefan/7769659/working/building/REAL300000078793 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078793

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078793/0 /scratch/stefan/7769659/working/building/REAL300000078793 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/799
`/scratch/stefan/7769659/working/3D/799' -> `0.mol2'
Preparing input files

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

`REAL300000078793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078793 none CC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 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: [127, 127, 127, 127, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 127, 127, 127, 128, 128, 128, 128, 128, 127, 127, 27, 27, 1, 1, 1, 127] 128
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078793 none CC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 66, 67, 128, 128, 128, 128, 128, 128, 128, 128, 128, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 8, 128, 128, 128, 1] 128
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078793 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078793/1 /scratch/stefan/7769659/working/building/REAL300000078793 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/800
`/scratch/stefan/7769659/working/3D/800' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1C(=O)[O-])

`REAL300000078793.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078793/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078793 none CC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 24, 24, 25, 25, 25, 25, 25, 24, 24, 15, 5, 1, 1, 1, 24] 25
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078793 none CC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 20, 24, 24, 24, 24, 24, 24, 24, 25, 25, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 20, 24, 24, 24, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078793 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078793
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078793/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078793/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078793
Building REAL300000078794
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078794'
/scratch/stefan/7769659/working/building/REAL300000078794 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078794

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078794/0 /scratch/stefan/7769659/working/building/REAL300000078794 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/801
`/scratch/stefan/7769659/working/3D/801' -> `0.mol2'
Preparing input files

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

`REAL300000078794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078794 none O=C([O-])C1=C(Cl)SC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 143, 142, 142, 142, 142, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 142, 27, 27, 1, 1, 1, 142] 143
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 27])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078794 none O=C([O-])C1=C(Cl)SC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 68, 69, 143, 143, 143, 143, 143, 143, 143, 143, 143, 1, 8, 8, 143, 143, 143, 1] 143
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078794 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078794
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078794/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078794
Building REAL300000078795
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078795'
/scratch/stefan/7769659/working/building/REAL300000078795 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078795

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078795/0 /scratch/stefan/7769659/working/building/REAL300000078795 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/802
`/scratch/stefan/7769659/working/3D/802' -> `0.mol2'
Preparing input files

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

`REAL300000078795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078795 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 19, 24, 24, 24, 24, 24, 19, 5, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 24, 24, 24, 24, 24, 19, 19, 19, 19, 1, 1, 1] 24
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078795 none CC1=CC(C(=O)[O-])=CC=C1C(C)N=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 11, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 24, 24, 24] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([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: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078795 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078795
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078795/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078795
Building REAL300000078796
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078796'
/scratch/stefan/7769659/working/building/REAL300000078796 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078796

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078796/0 /scratch/stefan/7769659/working/building/REAL300000078796 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/803
`/scratch/stefan/7769659/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078796 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 64, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 64, 64, 64, 64, 31, 31, 1, 1, 1] 64
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078796 none CN1N=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] 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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 64, 64, 64, 64, 64, 64, 64, 64, 64, 2, 2, 2, 1, 9, 9, 64, 64, 64] 64
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078796 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078796
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078796/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078796
Building REAL300000078797
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078797'
/scratch/stefan/7769659/working/building/REAL300000078797 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078797

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078797/0 /scratch/stefan/7769659/working/building/REAL300000078797 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/804
`/scratch/stefan/7769659/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])O2)=CC=C1O)

`REAL300000078797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078797 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [16, 13, 16, 13, 13, 1, 1, 1, 1, 1, 1, 8, 58, 58, 75, 75, 75, 75, 75, 75, 75, 76, 76, 1, 13, 13, 12, 12, 13, 1, 1, 8, 8, 75, 75, 75, 13, 13, 26] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078797 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 72, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 72, 72, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 3, 4, 5, 6, 24, 25, 26, 27, 28, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 410
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078797 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 75, 75, 75, 75, 20, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 75, 201, 201, 201, 201, 201, 75, 75, 20, 20, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 709
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078797 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078797
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078797/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078797
Building REAL300000078798
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078798'
/scratch/stefan/7769659/working/building/REAL300000078798 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078798

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078798/0 /scratch/stefan/7769659/working/building/REAL300000078798 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/805
`/scratch/stefan/7769659/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078798 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 62, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 62, 62, 62, 62, 62, 29, 29, 1, 1, 1] 62
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078798 none CN1C=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 1, 9, 42, 42, 62, 62, 62, 62, 62, 62, 62, 62, 62, 2, 2, 2, 1, 1, 9, 9, 62, 62, 62] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078798 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078798
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078798/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078798
Building REAL300000078799
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078799'
/scratch/stefan/7769659/working/building/REAL300000078799 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078799

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078799/0 /scratch/stefan/7769659/working/building/REAL300000078799 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/806
`/scratch/stefan/7769659/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078799 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 57, 57, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 57, 57, 57, 57, 57, 57, 57, 57, 57, 26, 26, 1, 1, 1] 57
rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 130
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078799 none CN(C)C1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 42, 43, 57, 57, 57, 57, 57, 57, 57, 57, 57, 4, 4, 4, 4, 4, 4, 1, 1, 1, 8, 8, 57, 57, 57] 57
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 114
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078799 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078799/1 /scratch/stefan/7769659/working/building/REAL300000078799 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/807
`/scratch/stefan/7769659/working/3D/807' -> `1.mol2'
Preparing input files

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

`REAL300000078799.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078799/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078799 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 1, 1, 1] 9
rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 20
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078799 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 8, 9, 9, 9] 9
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 10, 11, 12, 33, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 37
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078799 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078799
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078799/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078799/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078799
Building REAL300000078800
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078800'
/scratch/stefan/7769659/working/building/REAL300000078800 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078800

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078800/0 /scratch/stefan/7769659/working/building/REAL300000078800 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/808
`/scratch/stefan/7769659/working/3D/808' -> `0.mol2'
Preparing input files

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

`REAL300000078800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078800 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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: [132, 132, 132, 132, 133, 133, 132, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 132, 133, 133, 133, 132, 23, 23, 1, 1, 1] 133
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078800 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 74, 74, 132, 132, 132, 132, 132, 132, 132, 133, 133, 1, 2, 2, 2, 1, 8, 8, 132, 132, 132] 133
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 229
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078800 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078800
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078800/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078800
Building REAL300000078801
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078801'
/scratch/stefan/7769659/working/building/REAL300000078801 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078801

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078801/0 /scratch/stefan/7769659/working/building/REAL300000078801 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/809
`/scratch/stefan/7769659/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)C=C1)

`REAL300000078801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078801 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 61, 61, 90, 90, 90, 90, 90, 90, 90, 91, 91, 1, 7, 7, 7, 7, 1, 1, 8, 8, 90, 90, 90, 7, 7] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 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: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078801 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 41, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 41, 41, 201, 201, 201, 1, 1] 201
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: 347
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078801 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 119, 201, 119, 201, 201, 90, 90, 90, 90, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 90, 201, 201, 201, 201, 90, 90, 27, 27, 1, 1, 1, 201, 201] 201
rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 777
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078801 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078801
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078801/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078801
Building REAL300000078802
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078802'
/scratch/stefan/7769659/working/building/REAL300000078802 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078802

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078802/0 /scratch/stefan/7769659/working/building/REAL300000078802 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/810
`/scratch/stefan/7769659/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)=C1)

`REAL300000078802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078802 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 11, 12, 12, 1, 1, 1, 1, 1, 1, 9, 58, 58, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 12, 11, 12, 12, 1, 1, 9, 9, 73, 73, 73, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078802 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 67, 67, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078802 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 20, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 73, 201, 201, 201, 201, 73, 73, 20, 20, 1, 1, 1, 201] 201
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 312
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078802 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078802
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078802/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078802
Building REAL300000078803
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078803'
/scratch/stefan/7769659/working/building/REAL300000078803 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078803

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078803/0 /scratch/stefan/7769659/working/building/REAL300000078803 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/811
`/scratch/stefan/7769659/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078803 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 107, 107, 107, 107, 107, 107, 35, 35, 1, 1, 1] 107
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078803 none COC1=CC=C(C(=O)[O-])C=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 56, 57, 107, 107, 107, 107, 107, 107, 107, 107, 107, 4, 4, 4, 1, 1, 1, 8, 8, 107, 107, 107] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078803 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078803
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078803/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078803
Building REAL300000078804
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078804'
/scratch/stefan/7769659/working/building/REAL300000078804 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078804

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078804/0 /scratch/stefan/7769659/working/building/REAL300000078804 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/812
`/scratch/stefan/7769659/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1)

`REAL300000078804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078804 none O=C([O-])C1=CC=C2SC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 64, 64, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 64, 64, 64, 64, 64, 30, 30, 1, 1, 1, 64] 64
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078804 none O=C([O-])C1=CC=C2SC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 1, 8, 46, 46, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 8, 8, 64, 64, 64, 1] 64
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 23, 24, 25, 26, 27] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078804 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078804/1 /scratch/stefan/7769659/working/building/REAL300000078804 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/813
`/scratch/stefan/7769659/working/3D/813' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1)

`REAL300000078804.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078804/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078804 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 29, 28, 28, 28, 28, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 28, 29, 29, 28, 28, 21, 5, 1, 1, 1, 29] 29
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 48
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078804 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 29, 29, 29, 29, 29, 29, 28, 29, 29, 1, 1, 1, 1, 1, 10, 24, 29, 29, 29, 1] 29
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 23, 24, 25, 26, 27] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31])
total number of confs: 73
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078804 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078804
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078804/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078804/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078804
Building REAL300000078805
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078805'
/scratch/stefan/7769659/working/building/REAL300000078805 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078805

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078805/0 /scratch/stefan/7769659/working/building/REAL300000078805 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/814
`/scratch/stefan/7769659/working/3D/814' -> `0.mol2'
Preparing input files

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

`REAL300000078805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078805 none O=C([O-])C1=CN=C2CCCC(N=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.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, 8, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9] 9
rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078805 none O=C([O-])C1=CN=C2CCCC(N=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.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, 8, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 1] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36] set([33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 11
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078805 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078805
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078805/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078805
Building REAL300000078806
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078806'
/scratch/stefan/7769659/working/building/REAL300000078806 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078806

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078806/0 /scratch/stefan/7769659/working/building/REAL300000078806 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/815
`/scratch/stefan/7769659/working/3D/815' -> `0.mol2'
Preparing input files

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

`REAL300000078806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078806 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 25, 25, 1, 1, 1, 50] 50
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078806 none O=C([O-])C1=CC=C(Br)C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 8, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 8, 8, 50, 50, 50, 1] 50
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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
/scratch/stefan/7769659/working/building/REAL300000078806 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078806/1 /scratch/stefan/7769659/working/building/REAL300000078806 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/816
`/scratch/stefan/7769659/working/3D/816' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1)

`REAL300000078806.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078806/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078806 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 24, 24, 11, 3, 1, 1, 1, 24] 24
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 42
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078806 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 8, 24, 24, 24, 24, 1] 24
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078806 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078806
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078806/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078806/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078806
Building REAL300000078807
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078807'
/scratch/stefan/7769659/working/building/REAL300000078807 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078807

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078807/0 /scratch/stefan/7769659/working/building/REAL300000078807 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/817
`/scratch/stefan/7769659/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1C(=O)[O-])

`REAL300000078807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078807 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 123, 123, 123, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 123, 123, 122, 122, 201, 201, 201, 201, 201, 123, 23, 23, 1, 1, 1, 123, 123] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 674
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078807 none COC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 65, 65, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 9, 123, 123, 123, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078807 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078807
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078807/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078807
Building REAL300000078808
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078808'
/scratch/stefan/7769659/working/building/REAL300000078808 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078808

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078808/0 /scratch/stefan/7769659/working/building/REAL300000078808 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/818
`/scratch/stefan/7769659/working/3D/818' -> `0.mol2'
Preparing input files

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

`REAL300000078808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078808 none O=C([O-])C1=CC(F)=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 15, 39, 15, 38, 38, 38, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 38, 38, 38, 15, 15, 1, 1, 1, 38] 39
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078808 none O=C([O-])C1=CC(F)=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 1, 6, 29, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 6, 6, 39, 39, 39, 1] 39
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078808 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078808/1 /scratch/stefan/7769659/working/building/REAL300000078808 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/819
`/scratch/stefan/7769659/working/3D/819' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C(F)=C1)

`REAL300000078808.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078808/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078808 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 13, 12, 13, 13, 13, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 13, 13, 13, 12, 4, 1, 1, 1, 13] 13
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078808 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 1, 1, 1, 1, 6, 11, 11, 11, 11, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078808 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078808
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078808/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078808/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078808
Building REAL300000078809
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078809'
/scratch/stefan/7769659/working/building/REAL300000078809 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078809

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078809/0 /scratch/stefan/7769659/working/building/REAL300000078809 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/820
`/scratch/stefan/7769659/working/3D/820' -> `0.mol2'
Preparing input files

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

`REAL300000078809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078809 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 120, 120, 120, 120, 120, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 120, 120, 120, 120, 120, 27, 27, 1, 1, 1, 120] 120
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078809 none CC1=C(C(=O)[O-])NC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 69, 69, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 2, 2, 2, 1, 9, 9, 120, 120, 120, 1] 120
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25, 31] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078809 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078809
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078809/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078809
Building REAL300000078810
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078810'
/scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000078810

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078810/0 /scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/821
`/scratch/stefan/7769659/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1)

`REAL300000078810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 32, 10, 4, 1, 1, 1, 16] 32
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])
total number of confs: 62
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 8, 15, 16, 16, 16, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 43
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078810/1 /scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/822
`/scratch/stefan/7769659/working/3D/822' -> `1.mol2'
Preparing input files

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

`REAL300000078810.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078810/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C(O)C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 65, 65, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 65, 65, 130, 24, 24, 1, 1, 1, 65] 130
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])
total number of confs: 266
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C(O)C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 45, 45, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 2, 8, 8, 65, 65, 65, 1] 130
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 111
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `2'
/scratch/stefan/7769659/working/building/REAL300000078810/2 /scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 2 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/823
`/scratch/stefan/7769659/working/3D/823' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1)

`REAL300000078810.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000078810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078810/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 5, 1, 1, 1, 1, 6] 6
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 30])
total number of confs: 12
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078810 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 4, 6, 6, 6, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078810 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078810
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078810/0.*
2: /scratch/stefan/7769659/working/building/REAL300000078810/2.*
1: /scratch/stefan/7769659/working/building/REAL300000078810/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078810
Building REAL300000078811
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078811'
/scratch/stefan/7769659/working/building/REAL300000078811 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078811

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078811/0 /scratch/stefan/7769659/working/building/REAL300000078811 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/824
`/scratch/stefan/7769659/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)O1)

`REAL300000078811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078811 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 10, 11, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 9, 63, 63, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 10, 10, 10, 3, 3, 1, 1, 9, 9, 72, 72, 72, 1, 1] 201
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13, 40, 41, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 129
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078811 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 10, 10, 44, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 7, 7, 10, 10, 44, 44, 201, 201, 201, 10, 10] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 351
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078811 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 76, 72, 27, 17, 72, 72, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 72, 72, 201, 201, 201, 76, 76, 72, 72, 17, 17, 1, 1, 1, 72, 72] 201
rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 482
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078811 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078811
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078811/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078811
Building REAL300000078812
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078812'
/scratch/stefan/7769659/working/building/REAL300000078812 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078812

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078812/0 /scratch/stefan/7769659/working/building/REAL300000078812 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/825
`/scratch/stefan/7769659/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1O)

`REAL300000078812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078812 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 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, 56, 56, 56, 55, 56, 56, 56, 56, 56, 56, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 56, 56, 55, 56, 56, 56, 56, 27, 27, 1, 1, 1, 112] 112
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 246
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078812 none O=C([O-])C1=CC2=CC=CC=C2C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 42, 42, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 8, 8, 56, 56, 56, 2] 112
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 101
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078812 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078812/1 /scratch/stefan/7769659/working/building/REAL300000078812 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/826
`/scratch/stefan/7769659/working/3D/826' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1O)

`REAL300000078812.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078812/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078812 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 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, 34, 34, 34, 34, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 34, 34, 34, 34, 34, 34, 34, 16, 5, 1, 1, 1, 68] 68
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078812 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 11, 22, 34, 34, 34, 2] 68
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078812 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078812
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078812/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078812/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078812
Building REAL300000078813
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078813'
/scratch/stefan/7769659/working/building/REAL300000078813 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078813

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078813/0 /scratch/stefan/7769659/working/building/REAL300000078813 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/827
`/scratch/stefan/7769659/working/3D/827' -> `0.mol2'
Preparing input files

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

`REAL300000078813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078813 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 57, 58, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 93, 93, 93, 1, 1, 3] 201
rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 41, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43])
total number of confs: 187
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078813 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 107, 107, 123, 123, 123, 123, 123, 123, 123, 123, 123, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 123, 123, 123, 3, 3, 1] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 43, 28, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078813 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 123, 123, 123, 123, 123, 45, 31, 92, 92, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 92, 92, 123, 201, 201, 123, 123, 123, 92, 92, 31, 31, 1, 1, 1, 92, 92, 123] 201
rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43])
total number of confs: 889
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078813 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078813
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078813/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078813
Building REAL300000078814
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078814'
/scratch/stefan/7769659/working/building/REAL300000078814 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078814

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078814/0 /scratch/stefan/7769659/working/building/REAL300000078814 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/828
`/scratch/stefan/7769659/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CS1)

`REAL300000078814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078814 none O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 14, 15, 14, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 11, 5, 1, 1, 1, 14] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078814 none O=C([O-])C1=CC(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])=CS1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 14, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 6, 6, 12, 14, 14, 14, 14, 14, 14, 14, 15, 15, 1, 1, 1, 6, 12, 14, 14, 14, 1] 15
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078814 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078814
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078814/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078814
Building REAL300000078815
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078815'
/scratch/stefan/7769659/working/building/REAL300000078815 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078815

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078815/0 /scratch/stefan/7769659/working/building/REAL300000078815 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/829
`/scratch/stefan/7769659/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-])

`REAL300000078815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078815 none CCOC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 69, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 34, 34, 34, 34, 158, 201, 201, 201, 71, 71, 71, 71, 71, 34, 7, 7, 1, 1, 1, 34, 34, 201, 201] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41])
total number of confs: 557
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078815 none CCOC1=CC(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 35, 35, 1, 1, 1, 1, 7, 15, 25, 25, 5, 5, 5, 5, 5, 1, 6, 6, 34, 34, 34, 1, 1, 15, 15] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 38] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078815 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078815
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078815/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078815
Building REAL300000078816
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078816'
/scratch/stefan/7769659/working/building/REAL300000078816 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078816

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078816/0 /scratch/stefan/7769659/working/building/REAL300000078816 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/830
`/scratch/stefan/7769659/working/3D/830' -> `0.mol2'
Preparing input files

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

`REAL300000078816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078816 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 44, 44, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 63, 63, 63, 1, 1, 1, 1] 63
rigid atoms, others: [1, 34, 35, 36, 33, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078816 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 33, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 33, 33, 33, 33, 1, 1, 1, 63, 63, 63, 63] 63
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078816 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078816
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078816/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078816
Building REAL300000078817
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078817'
/scratch/stefan/7769659/working/building/REAL300000078817 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078817

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078817/0 /scratch/stefan/7769659/working/building/REAL300000078817 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/831
`/scratch/stefan/7769659/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1)

`REAL300000078817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078817 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 193, 82, 82, 82, 82, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 82, 201, 201, 193, 193, 82, 82, 19, 19, 1, 1, 1] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 701
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078817 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 14, 20, 8, 1, 1, 1, 1, 1, 1, 8, 57, 57, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 14, 14, 8, 8, 1, 1, 8, 8, 82, 82, 82] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078817 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078817
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078817/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078817
Building REAL300000078818
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078818'
/scratch/stefan/7769659/working/building/REAL300000078818 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078818

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078818/0 /scratch/stefan/7769659/working/building/REAL300000078818 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/832
`/scratch/stefan/7769659/working/3D/832' -> `0.mol2'
Preparing input files

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

`REAL300000078818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078818 none O=C([O-])C1=C2NC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 93, 93, 93, 93, 93, 93, 29, 29, 1, 1, 1, 93, 93, 93] 93
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078818 none O=C([O-])C1=C2NC=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C2=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 63, 64, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 9, 9, 93, 93, 93, 1, 1, 1] 93
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078818 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078818
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078818/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078818
Building REAL300000078819
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078819'
/scratch/stefan/7769659/working/building/REAL300000078819 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078819

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078819/0 /scratch/stefan/7769659/working/building/REAL300000078819 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/833
`/scratch/stefan/7769659/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=C(C(=O)[O-])C2=CC=CC=C2N=C1)

`REAL300000078819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078819 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 33, 33, 1, 1, 1, 1, 1] 33
rigid atoms, others: [1, 34, 35, 36, 37, 38, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078819 none CC(N=NC1=CC=CC(F)=C1[N+](=O)[O-])C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 1, 1, 1, 33, 33, 33, 33, 33] 33
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078819 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078819
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078819/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078819
Building REAL300000078820
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078820'
/scratch/stefan/7769659/working/building/REAL300000078820 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078820

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078820/0 /scratch/stefan/7769659/working/building/REAL300000078820 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/834
`/scratch/stefan/7769659/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=C2O1)

`REAL300000078820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078820 none O=C([O-])C1=CC2=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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, 89, 90, 89, 89, 89, 89, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 89, 89, 89, 89, 89, 89, 31, 31, 1, 1, 1, 89, 89] 90
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078820 none O=C([O-])C1=CC2=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=C2O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 60, 60, 89, 89, 89, 89, 89, 89, 89, 90, 90, 1, 1, 1, 1, 1, 1, 8, 8, 89, 89, 89, 1, 1] 90
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078820 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078820
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078820/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078820
Building REAL300000078821
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078821'
/scratch/stefan/7769659/working/building/REAL300000078821 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078821

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078821/0 /scratch/stefan/7769659/working/building/REAL300000078821 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/835
`/scratch/stefan/7769659/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12)

`REAL300000078821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078821 none O=C([O-])C1=CN=C2C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 75, 75, 75, 75, 75, 40, 40, 1, 1, 1, 75, 75, 75] 75
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078821 none O=C([O-])C1=CN=C2C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 9, 49, 49, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 9, 9, 75, 75, 75, 1, 1, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078821 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078821/1 /scratch/stefan/7769659/working/building/REAL300000078821 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/836
`/scratch/stefan/7769659/working/3D/836' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12)

`REAL300000078821.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078821/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078821 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 14, 9, 5, 1, 1, 1, 14, 14, 14] 15
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 28
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078821 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])=CC=CN12 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
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, 8, 12, 14, 14, 14, 14, 14, 14, 14, 15, 15, 1, 1, 1, 1, 1, 8, 12, 14, 14, 14, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078821 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078821
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078821/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078821/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078821
Building REAL300000078822
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078822'
/scratch/stefan/7769659/working/building/REAL300000078822 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078822

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078822/0 /scratch/stefan/7769659/working/building/REAL300000078822 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/837
`/scratch/stefan/7769659/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1)

`REAL300000078822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078822 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [88, 87, 88, 87, 87, 87, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 63, 63, 63, 63, 63, 63, 63, 63, 63, 87, 87, 87, 31, 31, 1, 1, 1, 1, 7, 7, 63, 63, 63] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41])
total number of confs: 282
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078822 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 37, 87, 87, 55, 87, 87, 87, 113, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 87, 87, 87, 87, 113, 113, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 550
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078822 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=C2[N+](=O)[O-])O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 112, 63, 63, 63, 38, 63, 63, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 201, 201, 201, 169, 169, 63, 62, 63, 63, 32, 32, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 675
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078822 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078822
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078822/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078822
Building REAL300000078823
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078823'
/scratch/stefan/7769659/working/building/REAL300000078823 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078823

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078823/0 /scratch/stefan/7769659/working/building/REAL300000078823 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/838
`/scratch/stefan/7769659/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl)

`REAL300000078823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078823 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 165, 50, 50, 51, 51, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 51, 51, 51, 201, 201, 51, 51, 13, 13, 1, 1, 1, 51] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078823 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [35, 25, 35, 7, 1, 1, 1, 1, 1, 1, 9, 45, 45, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 25, 25, 1, 1, 9, 9, 51, 51, 51, 1] 201
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078823 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078823/1 /scratch/stefan/7769659/working/building/REAL300000078823 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/839
`/scratch/stefan/7769659/working/3D/839' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl)

`REAL300000078823.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078823/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078823 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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
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, 100, 25, 25, 25, 25, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 25, 152, 152, 25, 25, 11, 5, 1, 1, 1, 25] 152
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 429
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078823 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=C2[N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [62, 40, 62, 9, 1, 1, 1, 1, 1, 1, 6, 6, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 40, 40, 1, 1, 6, 12, 25, 25, 25, 1] 152
rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 259
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078823 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078823
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078823/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078823/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078823
Building REAL300000078824
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078824'
/scratch/stefan/7769659/working/building/REAL300000078824 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078824

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078824/0 /scratch/stefan/7769659/working/building/REAL300000078824 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/840
`/scratch/stefan/7769659/working/3D/840' -> `0.mol2'
Preparing input files

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

`REAL300000078824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078824 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.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, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 176, 96, 44, 96, 96, 33, 95, 88, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 95, 95, 197, 197, 176, 95, 95, 21, 21, 1, 1, 1, 95, 95] 197
rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 968
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078824 none O=C([O-])CNS(=O)(=O)C1=CC=C(CN=NC2=CC=CC(F)=C2[N+](=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.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, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [11, 9, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 62, 62, 95, 95, 95, 95, 95, 95, 95, 96, 96, 1, 1, 9, 9, 5, 1, 1, 8, 8, 95, 95, 95, 1, 1] 197
rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 25, 26, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078824 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078824
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078824/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078824
Building REAL300000078825
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078825'
/scratch/stefan/7769659/working/building/REAL300000078825 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078825

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078825/0 /scratch/stefan/7769659/working/building/REAL300000078825 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/841
`/scratch/stefan/7769659/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1)

`REAL300000078825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078825 none O=C([O-])C1=CC2=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 63, 63, 63, 62, 63, 63, 63, 25, 25, 1, 1, 1, 63, 62] 63
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078825 none O=C([O-])C1=CC2=C(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 52, 52, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 8, 8, 63, 63, 63, 1, 1] 63
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078825 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078825/1 /scratch/stefan/7769659/working/building/REAL300000078825 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/842
`/scratch/stefan/7769659/working/3D/842' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1)

`REAL300000078825.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078825/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078825 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 41, 42, 41, 41, 41, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 41, 41, 41, 41, 41, 41, 41, 17, 5, 1, 1, 1, 41, 41] 42
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078825 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(F)=C3[N+](=O)[O-])C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 31, 41, 41, 41, 41, 41, 41, 41, 42, 42, 1, 1, 1, 1, 1, 1, 1, 12, 31, 41, 41, 41, 1, 1] 42
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078825 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078825
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078825/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078825/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078825
Building REAL300000078826
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078826'
/scratch/stefan/7769659/working/building/REAL300000078826 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078826

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078826/0 /scratch/stefan/7769659/working/building/REAL300000078826 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/843
`/scratch/stefan/7769659/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-])

`REAL300000078826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078826 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 98, 98, 98, 96, 98, 98, 98, 98, 98, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 98, 98, 98, 98, 98, 98, 31, 31, 1, 1, 1] 98
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078826 none COC1=CC(C(=O)[O-])=CC=C1CN=NC1=CC=CC(F)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 57, 58, 98, 98, 98, 98, 98, 98, 98, 98, 98, 3, 3, 3, 1, 1, 1, 8, 8, 98, 98, 98] 98
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078826 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078826
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078826/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078826
Building REAL300000078827
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078827'
/scratch/stefan/7769659/working/building/REAL300000078827 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078827

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078827/0 /scratch/stefan/7769659/working/building/REAL300000078827 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/844
`/scratch/stefan/7769659/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=N2)C1)

`REAL300000078827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078827 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 21, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 9, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 11, 11, 11, 1, 1, 9, 9, 50, 50, 50, 11, 11] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078827 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 11, 1, 1, 1, 11, 11, 61, 61, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 36, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078827 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=C3[N+](=O)[O-])=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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
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, 50, 201, 50, 50, 50, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 201, 201, 201, 50, 50, 11, 12, 1, 1, 1, 201, 201] 201
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])
total number of confs: 461
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078827 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078827
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078827/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078827
Building REAL300000078828
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078828'
/scratch/stefan/7769659/working/building/REAL300000078828 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078828

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078828/0 /scratch/stefan/7769659/working/building/REAL300000078828 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/845
`/scratch/stefan/7769659/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 23, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 12, 11, 12, 11, 1, 1, 6, 6, 6, 23, 33, 33, 33, 1, 1, 12, 12, 1, 1] 54
rigid atoms, others: [32, 1, 36, 37, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 92
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 27, 27, 54, 54, 54, 54, 54, 54, 54, 33, 33, 19, 19, 19, 4, 1, 1, 1, 33, 33, 54, 54, 33, 33] 54
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [20, 1, 20, 26, 52, 54, 54, 54, 54, 54, 54, 1, 11, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 20, 25, 25, 52, 54, 54, 54, 12, 12, 1, 1, 12, 12] 54
rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 194
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078828 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078828/1 /scratch/stefan/7769659/working/building/REAL300000078828 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/846
`/scratch/stefan/7769659/working/3D/846' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078828.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078828/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 49, 49, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 7, 110, 110, 110, 1, 1, 12, 12, 1, 1] 197
rigid atoms, others: [32, 1, 36, 37, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 54, 110, 110, 76, 77, 197, 197, 197, 197, 197, 197, 197, 110, 110, 54, 54, 54, 54, 1, 1, 1, 110, 110, 196, 197, 110, 110] 197
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078828 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 1, 18, 139, 136, 195, 194, 195, 195, 196, 197, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 18, 19, 17, 15, 195, 195, 196, 12, 12, 1, 1, 12, 12] 197
rigid atoms, others: [34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 350
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078828 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078828
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078828/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078828/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078828
Building REAL300000078829
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078829'
/scratch/stefan/7769659/working/building/REAL300000078829 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078829

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078829/0 /scratch/stefan/7769659/working/building/REAL300000078829 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/847
`/scratch/stefan/7769659/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-])

`REAL300000078829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078829 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 40, 40, 40, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 127, 200, 201, 201, 68, 68, 68, 40, 14, 4, 1, 1, 1, 40, 40, 200, 200] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 573
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078829 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 25, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 9, 41, 74, 74, 3, 3, 3, 1, 9, 25, 40, 40, 40, 1, 1, 41, 41] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078829 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078829/1 /scratch/stefan/7769659/working/building/REAL300000078829 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/848
`/scratch/stefan/7769659/working/3D/848' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-])

`REAL300000078829.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078829/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078829 none COC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 48, 48, 48, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 134, 201, 201, 201, 86, 86, 86, 48, 15, 15, 1, 1, 1, 48, 48, 201, 201] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 637
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078829 none COC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 42, 42, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 9, 23, 28, 28, 3, 3, 3, 1, 6, 6, 48, 48, 48, 1, 1, 23, 23] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078829 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078829
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078829/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078829/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078829
Building REAL300000078830
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078830'
/scratch/stefan/7769659/working/building/REAL300000078830 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078830

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078830/0 /scratch/stefan/7769659/working/building/REAL300000078830 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/849
`/scratch/stefan/7769659/working/3D/849' -> `0.mol2'
Preparing input files

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

`REAL300000078830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078830 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 6, 26, 44, 44, 1, 11, 11, 11, 41, 57, 57, 57, 1, 1, 1, 26, 26, 1] 201
rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 259
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078830 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 57, 57, 57, 57, 57, 138, 201, 201, 201, 57, 14, 14, 14, 4, 1, 1, 1, 57, 57, 57, 201, 201, 57] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 526
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078830 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078830/1 /scratch/stefan/7769659/working/building/REAL300000078830 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/850
`/scratch/stefan/7769659/working/3D/850' -> `1.mol2'
Preparing input files

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

`REAL300000078830.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078830/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078830 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 34, 34, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 7, 20, 32, 32, 1, 7, 7, 7, 7, 54, 54, 54, 1, 1, 1, 20, 20, 1] 201
rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 189
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078830 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 54, 54, 54, 54, 54, 146, 201, 201, 201, 54, 21, 21, 21, 21, 1, 1, 1, 54, 54, 54, 201, 201, 54] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 547
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078830 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078830
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078830/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078830/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078830
Building REAL300000078831
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078831'
/scratch/stefan/7769659/working/building/REAL300000078831 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078831

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078831/0 /scratch/stefan/7769659/working/building/REAL300000078831 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/851
`/scratch/stefan/7769659/working/3D/851' -> `0.mol2'
Preparing input files

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

`REAL300000078831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078831 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 7, 7, 7, 20, 20, 20, 20, 1, 1, 9, 17, 17, 1, 1] 54
rigid atoms, others: [32, 1, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078831 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 6, 6, 32, 32, 32, 45, 54, 54, 54, 20, 20, 6, 6, 6, 2, 1, 1, 1, 20, 20, 45, 54, 54, 20, 20] 54
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078831 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078831/1 /scratch/stefan/7769659/working/building/REAL300000078831 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/852
`/scratch/stefan/7769659/working/3D/852' -> `1.mol2'
Preparing input files

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

`REAL300000078831.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078831/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078831 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 23, 23, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 5, 5, 5, 5, 66, 66, 66, 1, 1, 9, 17, 17, 1, 1] 187
rigid atoms, others: [32, 1, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078831 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 66, 66, 35, 35, 108, 108, 108, 182, 187, 187, 187, 66, 66, 35, 35, 35, 35, 1, 1, 1, 66, 66, 182, 187, 187, 66, 66] 187
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 839
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078831 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078831
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078831/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078831/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078831
Building REAL300000078832
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078832'
/scratch/stefan/7769659/working/building/REAL300000078832 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078832

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078832/0 /scratch/stefan/7769659/working/building/REAL300000078832 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/853
`/scratch/stefan/7769659/working/3D/853' -> `0.mol2'
Preparing input files

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

`REAL300000078832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078832 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 7, 7, 7, 7, 1, 1, 9, 9, 9, 9, 9, 1, 1] 29
rigid atoms, others: [1, 34, 33, 40, 41, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 43
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078832 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 6, 13, 13, 13, 29, 29, 29, 29, 29, 7, 7, 6, 6, 6, 2, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 7, 7] 29
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 99
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078832 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078832/1 /scratch/stefan/7769659/working/building/REAL300000078832 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/854
`/scratch/stefan/7769659/working/3D/854' -> `1.mol2'
Preparing input files

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

`REAL300000078832.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078832/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078832 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 19, 19, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 4, 4, 4, 4, 34, 34, 34, 1, 1, 9, 9, 9, 9, 9, 1, 1] 93
rigid atoms, others: [1, 34, 33, 40, 41, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078832 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 20, 19, 45, 45, 45, 93, 93, 93, 93, 93, 34, 34, 19, 19, 19, 19, 1, 1, 1, 34, 34, 93, 93, 93, 93, 93, 34, 34] 93
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078832 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078832
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078832/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078832/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078832
Building REAL300000078833
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078833'
/scratch/stefan/7769659/working/building/REAL300000078833 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078833

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078833/0 /scratch/stefan/7769659/working/building/REAL300000078833 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/855
`/scratch/stefan/7769659/working/3D/855' -> `0.mol2'
Preparing input files

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

`REAL300000078833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078833 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCCC(=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 11, 11, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 27
rigid atoms, others: [1, 34, 35, 44, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 47
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078833 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCCC(=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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 10, 10, 19, 19, 19, 27, 27, 27, 27, 27, 27, 11, 11, 10, 10, 10, 4, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 11, 11] 27
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 101
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078833 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078833/1 /scratch/stefan/7769659/working/building/REAL300000078833 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/856
`/scratch/stefan/7769659/working/3D/856' -> `1.mol2'
Preparing input files

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

`REAL300000078833.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078833/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078833 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 4, 16, 16, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 22, 22, 22, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 51
rigid atoms, others: [1, 34, 35, 44, 11, 12, 13, 14, 15, 43, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 56
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078833 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 13, 13, 34, 34, 34, 51, 51, 51, 51, 51, 51, 22, 22, 13, 13, 13, 13, 1, 1, 1, 22, 22, 51, 51, 51, 51, 51, 51, 51, 22, 22] 51
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 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
/scratch/stefan/7769659/working/building/REAL300000078833 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078833
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078833/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078833/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078833
Building REAL300000078834
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078834'
/scratch/stefan/7769659/working/building/REAL300000078834 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078834

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078834/0 /scratch/stefan/7769659/working/building/REAL300000078834 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/857
`/scratch/stefan/7769659/working/3D/857' -> `0.mol2'
Preparing input files

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

`REAL300000078834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078834 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 1] 9
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 23
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078834 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 2, 1, 1, 1, 3, 3, 9, 9, 9, 9, 3, 3] 9
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 35
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078834 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078834/1 /scratch/stefan/7769659/working/building/REAL300000078834 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/858
`/scratch/stefan/7769659/working/3D/858' -> `1.mol2'
Preparing input files

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

`REAL300000078834.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078834/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078834 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 5, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1] 13
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 30
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078834 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 3, 3, 8, 8, 8, 13, 13, 13, 13, 13, 13, 5, 5, 3, 3, 3, 3, 1, 1, 1, 5, 5, 13, 13, 13, 13, 5, 5] 13
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078834 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078834
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078834/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078834/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078834
Building REAL300000078835
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078835'
/scratch/stefan/7769659/working/building/REAL300000078835 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078835

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078835/0 /scratch/stefan/7769659/working/building/REAL300000078835 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/859
`/scratch/stefan/7769659/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC(F)=N1)CCC2)

`REAL300000078835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078835 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC(F)=N1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9] 9
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 14
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078835 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC(F)=N1)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 8, 9, 9, 9, 1, 1, 1, 1, 1, 1] 9
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 29, 30, 31] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 29
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078835 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078835
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078835/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078835
Building REAL300000078836
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078836'
/scratch/stefan/7769659/working/building/REAL300000078836 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078836

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078836/0 /scratch/stefan/7769659/working/building/REAL300000078836 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/860
`/scratch/stefan/7769659/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1)

`REAL300000078836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078836 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 139, 120, 78, 19, 19, 60, 60, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 141, 141, 120, 120, 60, 60, 19, 4, 1, 1, 1, 60, 60] 141
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 530
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078836 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [40, 28, 34, 15, 3, 1, 1, 1, 1, 1, 1, 11, 11, 43, 60, 60, 60, 60, 60, 60, 1, 1, 27, 27, 15, 15, 1, 1, 11, 43, 60, 60, 60, 1, 1] 141
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 279
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078836 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078836/1 /scratch/stefan/7769659/working/building/REAL300000078836 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/861
`/scratch/stefan/7769659/working/3D/861' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1)

`REAL300000078836.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078836/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078836 none O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 198, 165, 51, 18, 87, 87, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 200, 200, 199, 199, 87, 87, 18, 18, 1, 1, 1, 87, 87] 201
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 668
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078836 none O=C([O-])CCOC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 14, 17, 11, 3, 1, 1, 1, 1, 1, 1, 8, 51, 51, 87, 87, 87, 87, 87, 87, 1, 1, 13, 13, 12, 11, 1, 1, 8, 8, 87, 87, 87, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 209
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078836 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078836
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078836/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078836/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078836
Building REAL300000078837
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078837'
/scratch/stefan/7769659/working/building/REAL300000078837 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078837

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078837/0 /scratch/stefan/7769659/working/building/REAL300000078837 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/862
`/scratch/stefan/7769659/working/3D/862' -> `0.mol2'
Preparing input files

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

`REAL300000078837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078837 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 148, 105, 37, 37, 37, 18, 37, 37, 37, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 37, 37, 37, 18, 5, 1, 1, 1] 148
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 459
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078837 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [81, 49, 81, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 37, 37, 37, 37, 37, 37, 49, 49, 1, 1, 1, 4, 22, 37, 37, 37] 148
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 334
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078837 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078837/1 /scratch/stefan/7769659/working/building/REAL300000078837 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/863
`/scratch/stefan/7769659/working/3D/863' -> `1.mol2'
Preparing input files

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

`REAL300000078837.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078837/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078837 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 143, 65, 65, 65, 42, 65, 65, 65, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 65, 65, 65, 20, 21, 1, 1, 1] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 649
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078837 none O=C([O-])COC1=CC=C(Br)C=C1CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 34, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 45, 46, 65, 65, 65, 65, 65, 65, 34, 34, 1, 1, 1, 8, 8, 65, 65, 65] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078837 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078837
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078837/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078837/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078837
Building REAL300000078838
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078838'
/scratch/stefan/7769659/working/building/REAL300000078838 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078838

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078838/0 /scratch/stefan/7769659/working/building/REAL300000078838 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/864
`/scratch/stefan/7769659/working/3D/864' -> `0.mol2'
Preparing input files

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

`REAL300000078838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078838 none CC(OC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 151, 51, 51, 51, 51, 51, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 17, 4, 1, 1, 1, 51] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 476
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078838 none CC(OC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 51, 51, 51, 51, 51, 51, 1, 34, 54, 54, 34, 34, 34, 34, 1, 1, 1, 10, 33, 51, 51, 51, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 301
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078838 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078838/1 /scratch/stefan/7769659/working/building/REAL300000078838 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/865
`/scratch/stefan/7769659/working/3D/865' -> `1.mol2'
Preparing input files

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

`REAL300000078838.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078838/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078838 none CC(OC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 150, 50, 50, 50, 50, 50, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 17, 18, 1, 1, 1, 50] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 527
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078838 none CC(OC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 11, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 50, 50, 50, 50, 50, 50, 1, 27, 36, 36, 27, 27, 27, 27, 1, 1, 1, 8, 8, 50, 50, 50, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 18, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 195
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078838 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078838
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078838/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078838/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078838
Building REAL300000078839
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078839'
/scratch/stefan/7769659/working/building/REAL300000078839 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078839

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078839/0 /scratch/stefan/7769659/working/building/REAL300000078839 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/866
`/scratch/stefan/7769659/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)

`REAL300000078839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078839 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 169, 109, 51, 51, 51, 51, 51, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 169, 169, 51, 51, 51, 15, 4, 1, 1, 1, 51] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 595
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078839 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 45, 59, 26, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 51, 51, 51, 51, 51, 51, 1, 45, 45, 26, 26, 1, 1, 1, 12, 33, 51, 51, 51, 1] 201
rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 361
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078839 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078839/1 /scratch/stefan/7769659/working/building/REAL300000078839 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/867
`/scratch/stefan/7769659/working/3D/867' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)

`REAL300000078839.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078839/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078839 none O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 201, 189, 58, 58, 58, 58, 58, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 58, 58, 58, 18, 19, 1, 1, 1, 58] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 361
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078839 none O=C([O-])CCOC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 14, 19, 14, 6, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 58, 58, 58, 58, 58, 58, 1, 14, 14, 14, 14, 1, 1, 1, 7, 7, 58, 58, 58, 1] 201
rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33])
total number of confs: 172
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078839 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078839
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078839/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078839/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078839
Building REAL300000078840
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078840'
/scratch/stefan/7769659/working/building/REAL300000078840 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078840

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078840/0 /scratch/stefan/7769659/working/building/REAL300000078840 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/868
`/scratch/stefan/7769659/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)

`REAL300000078840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [22, 17, 22, 17, 17, 17, 17, 17, 7, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 35, 35, 35, 35, 35, 35, 1, 17, 17, 17, 17, 7, 7, 1, 1, 1, 8, 26, 35, 35, 35, 1] 96
rigid atoms, others: [33, 34, 35, 41, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 136
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 17, 17, 17, 17, 17, 59, 59, 89, 96, 96, 96, 96, 96, 96, 17, 1, 1, 1, 1, 5, 5, 17, 17, 17, 59, 88, 96, 96, 96, 17] 96
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 255
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 96, 96, 96, 96, 96, 96, 53, 48, 35, 35, 35, 35, 35, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 35, 96, 96, 96, 96, 53, 53, 35, 35, 35, 18, 4, 1, 1, 1, 35] 96
rigid atoms, others: [38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 163
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078840 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078840/1 /scratch/stefan/7769659/working/building/REAL300000078840 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/869
`/scratch/stefan/7769659/working/3D/869' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)

`REAL300000078840.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078840/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 8, 11, 8, 8, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 1, 7, 55, 56, 98, 98, 98, 98, 98, 98, 1, 8, 8, 8, 8, 4, 4, 1, 1, 1, 7, 7, 98, 98, 98, 1] 201
rigid atoms, others: [33, 34, 35, 41, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40])
total number of confs: 186
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 5, 8, 8, 40, 152, 153, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 3, 3, 8, 8, 8, 40, 40, 201, 201, 201, 8] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 395
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078840 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 155, 153, 98, 98, 98, 98, 98, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 155, 155, 98, 98, 98, 20, 21, 1, 1, 1, 98] 201
rigid atoms, others: [38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 357
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078840 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078840
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078840/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078840/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078840
Building REAL300000078841
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078841'
/scratch/stefan/7769659/working/building/REAL300000078841 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078841

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078841/0 /scratch/stefan/7769659/working/building/REAL300000078841 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/870
`/scratch/stefan/7769659/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1[N+](=O)[O-])

`REAL300000078841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078841 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 7, 7, 9, 9, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 9, 9, 4, 2, 1, 1, 1, 9] 15
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078841 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 9, 9, 9, 9, 1] 15
rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078841 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078841
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078841/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078841
Building REAL300000078842
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078842'
/scratch/stefan/7769659/working/building/REAL300000078842 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078842

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078842/0 /scratch/stefan/7769659/working/building/REAL300000078842 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/871
`/scratch/stefan/7769659/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1)

`REAL300000078842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 47, 47, 80, 80, 80, 80, 80, 80, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 80, 80, 80, 1, 1, 6] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 31, 153, 153, 201, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 6, 6, 6, 6, 31, 31, 201, 201, 201, 5, 6, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 362
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 28, 80, 80, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 81, 81, 80, 80, 20, 20, 1, 1, 1, 80, 80, 201] 201
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078842 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078842/1 /scratch/stefan/7769659/working/building/REAL300000078842 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/872
`/scratch/stefan/7769659/working/3D/872' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1)

`REAL300000078842.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078842/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 51, 51, 29, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 41, 41, 41, 41, 41, 41, 1, 1, 29, 29, 29, 29, 7, 7, 1, 1, 9, 33, 41, 41, 41, 1, 1, 29] 201
rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41])
total number of confs: 227
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 29, 29, 29, 29, 29, 114, 114, 169, 201, 201, 201, 201, 201, 201, 29, 29, 1, 2, 2, 2, 9, 9, 29, 29, 114, 169, 201, 201, 201, 28, 29, 1] 201
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 537
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078842 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 76, 41, 16, 16, 41, 41, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 76, 76, 41, 41, 16, 4, 1, 1, 1, 41, 41, 201] 201
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41])
total number of confs: 455
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078842 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078842
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078842/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078842/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078842
Building REAL300000078843
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078843'
/scratch/stefan/7769659/working/building/REAL300000078843 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078843

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078843/0 /scratch/stefan/7769659/working/building/REAL300000078843 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/873
`/scratch/stefan/7769659/working/3D/873' -> `0.mol2'
Preparing input files

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

`REAL300000078843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 30, 31, 31, 8, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 24, 24, 24, 24, 24, 24, 1, 31, 30, 31, 31, 8, 8, 1, 1, 1, 10, 22, 24, 24, 24, 1, 31] 201
rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 41])
total number of confs: 121
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 31, 31, 31, 31, 31, 154, 154, 201, 201, 201, 201, 201, 201, 201, 31, 1, 1, 1, 1, 9, 9, 31, 31, 31, 154, 201, 201, 201, 201, 31, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 527
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 60, 38, 24, 24, 24, 24, 24, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 60, 60, 24, 24, 24, 12, 4, 1, 1, 1, 24, 201] 201
rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 337
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078843 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078843/1 /scratch/stefan/7769659/working/building/REAL300000078843 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/874
`/scratch/stefan/7769659/working/3D/874' -> `1.mol2'
Preparing input files

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

`REAL300000078843.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078843/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 14, 15, 15, 4, 2, 1, 1, 1, 1, 1, 1, 1, 8, 43, 43, 56, 56, 56, 56, 56, 56, 1, 15, 14, 15, 15, 4, 4, 1, 1, 1, 8, 8, 56, 56, 56, 1, 15] 201
rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 41])
total number of confs: 119
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 15, 65, 187, 187, 201, 201, 201, 201, 201, 201, 15, 1, 1, 1, 1, 8, 8, 15, 14, 15, 65, 65, 201, 201, 201, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 423
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078843 none O=C([O-])C1=CC=CC(COC2=CC=CC(CN=NC3=CC=CC(F)=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 91, 89, 56, 56, 56, 56, 56, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 91, 91, 56, 56, 56, 18, 19, 1, 1, 1, 56, 201] 201
rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 346
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078843 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078843
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078843/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078843/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078843
Building REAL300000078844
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078844'
/scratch/stefan/7769659/working/building/REAL300000078844 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078844

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078844/0 /scratch/stefan/7769659/working/building/REAL300000078844 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/875
`/scratch/stefan/7769659/working/3D/875' -> `0.mol2'
Preparing input files

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

`REAL300000078844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 8, 63, 63, 132, 132, 132, 132, 132, 132, 1, 1, 7, 7, 7, 3, 3, 1, 1, 8, 8, 132, 132, 132, 1, 1, 7, 7] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 223
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 5, 7, 7, 7, 7, 7, 41, 166, 167, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 5, 5, 7, 7, 41, 41, 201, 201, 201, 7, 7, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 38, 23, 24, 25, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 374
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 139, 132, 132, 45, 132, 132, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 201, 201, 201, 140, 140, 132, 132, 36, 36, 1, 1, 1, 132, 132, 201, 201] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 643
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078844 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078844/1 /scratch/stefan/7769659/working/building/REAL300000078844 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/876
`/scratch/stefan/7769659/working/3D/876' -> `1.mol2'
Preparing input files

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

`REAL300000078844.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078844/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
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: [14, 12, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 23, 25, 25, 25, 25, 25, 25, 1, 1, 11, 11, 11, 5, 5, 1, 1, 9, 23, 25, 25, 25, 1, 1, 11, 11] 51
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 96
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 11, 11, 11, 11, 11, 39, 39, 49, 51, 51, 51, 51, 51, 51, 11, 11, 1, 1, 1, 5, 5, 11, 11, 39, 49, 51, 51, 51, 11, 11, 1, 1] 51
rigid atoms, others: [1, 3, 4, 5, 38, 23, 24, 25, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 141
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078844 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)OC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
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, 35, 25, 12, 12, 25, 25, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 51, 51, 51, 35, 35, 25, 25, 12, 4, 1, 1, 1, 25, 25, 51, 51] 51
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 161
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078844 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078844
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078844/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078844/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078844
Building REAL300000078845
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078845'
/scratch/stefan/7769659/working/building/REAL300000078845 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078845

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078845/0 /scratch/stefan/7769659/working/building/REAL300000078845 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/877
`/scratch/stefan/7769659/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1)

`REAL300000078845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078845 none COC1=CC=C(C=NNC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [60, 37, 20, 37, 37, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 104, 182, 192, 192, 37, 60, 60, 60, 37, 37, 18, 4, 1, 1, 1, 182, 182, 37] 192
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 671
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078845 none COC1=CC=C(C=NNC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 19, 37, 37, 37, 37, 37, 37, 1, 1, 9, 49, 86, 86, 1, 3, 3, 3, 1, 1, 6, 19, 37, 37, 37, 49, 49, 1] 192
rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 35, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 359
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078845 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078845/1 /scratch/stefan/7769659/working/building/REAL300000078845 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/878
`/scratch/stefan/7769659/working/3D/878' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN=NC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1)

`REAL300000078845.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078845/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078845 none COC1=CC=C(CN=NC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 68, 40, 68, 68, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 139, 199, 201, 201, 68, 82, 82, 82, 68, 68, 25, 25, 1, 1, 1, 199, 199, 68] 201
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 704
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078845 none COC1=CC=C(CN=NC2=CC=CC(F)=N2)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 42, 42, 68, 68, 68, 68, 68, 68, 1, 1, 7, 26, 43, 43, 1, 3, 3, 3, 1, 1, 8, 8, 68, 68, 68, 26, 26, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 35, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078845 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078845
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078845/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078845/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078845
Building REAL300000078846
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078846'
/scratch/stefan/7769659/working/building/REAL300000078846 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078846

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078846/0 /scratch/stefan/7769659/working/building/REAL300000078846 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/879
`/scratch/stefan/7769659/working/3D/879' -> `0.mol2'
Preparing input files

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

`REAL300000078846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078846 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 196, 201, 105, 196, 196, 18, 18, 62, 62, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 18, 4, 1, 1, 1, 62, 62] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 693
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078846 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 31, 54, 7, 31, 31, 1, 1, 1, 1, 1, 1, 10, 10, 38, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 10, 38, 62, 62, 62, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 318
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078846 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078846/1 /scratch/stefan/7769659/working/building/REAL300000078846 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/880
`/scratch/stefan/7769659/working/3D/880' -> `1.mol2'
Preparing input files

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

`REAL300000078846.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078846/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078846 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 130, 201, 201, 31, 12, 49, 49, 12, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 12, 12, 1, 1, 1, 49, 49] 201
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 661
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078846 none O=C([O-])C(F)(F)OC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 19, 25, 6, 19, 19, 1, 1, 1, 1, 1, 1, 6, 45, 45, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 6, 6, 49, 49, 49, 1, 1] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 150
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078846 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078846
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078846/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078846/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078846
Building REAL300000078847
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078847'
/scratch/stefan/7769659/working/building/REAL300000078847 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078847

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078847/0 /scratch/stefan/7769659/working/building/REAL300000078847 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/881
`/scratch/stefan/7769659/working/3D/881' -> `0.mol2'
Preparing input files

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

`REAL300000078847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078847 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 12, 12, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 8, 4, 1, 1, 1] 12
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078847 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 8, 12, 12, 12, 12] 12
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078847 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078847
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078847/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078847
Building REAL300000078848
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078848'
/scratch/stefan/7769659/working/building/REAL300000078848 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078848

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078848/0 /scratch/stefan/7769659/working/building/REAL300000078848 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/882
`/scratch/stefan/7769659/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1Br)

`REAL300000078848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078848 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 145, 63, 32, 63, 63, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 201, 201, 63, 63, 19, 4, 1, 1, 1, 63] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 625
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078848 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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: [76, 45, 76, 9, 1, 1, 1, 1, 1, 1, 7, 7, 36, 63, 63, 63, 63, 63, 63, 1, 1, 1, 45, 45, 1, 1, 7, 36, 63, 63, 63, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 366
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078848 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078848/1 /scratch/stefan/7769659/working/building/REAL300000078848 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/883
`/scratch/stefan/7769659/working/3D/883' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1Br)

`REAL300000078848.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078848/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078848 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 176, 77, 33, 77, 77, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 201, 201, 77, 77, 16, 17, 1, 1, 1, 77] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 600
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078848 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1Br NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 24, 34, 7, 1, 1, 1, 1, 1, 1, 7, 47, 47, 77, 77, 77, 77, 77, 77, 1, 1, 1, 24, 24, 1, 1, 7, 7, 77, 77, 77, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078848 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078848
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078848/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078848/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078848
Building REAL300000078849
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078849'
/scratch/stefan/7769659/working/building/REAL300000078849 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078849

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078849/0 /scratch/stefan/7769659/working/building/REAL300000078849 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/884
`/scratch/stefan/7769659/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=N2)C=C1)

`REAL300000078849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078849 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 14, 4, 1, 1, 1, 23, 23] 23
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078849 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 22, 23, 23, 23, 23, 23, 23, 1, 1, 3, 3, 3, 1, 8, 22, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 12, 34, 22, 23, 27] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078849 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078849
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078849/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078849
Building REAL300000078850
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078850'
/scratch/stefan/7769659/working/building/REAL300000078850 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078850

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078850/0 /scratch/stefan/7769659/working/building/REAL300000078850 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/885
`/scratch/stefan/7769659/working/3D/885' -> `0.mol2'
Preparing input files

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

`REAL300000078850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078850 none CCC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [30, 12, 1, 12, 12, 56, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 31, 31, 31, 30, 30, 56, 69, 69, 69, 1, 1, 1] 74
rigid atoms, others: [32, 33, 2, 12, 13, 14, 15, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 262
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078850 none CCC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [42, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 20, 69, 69, 69, 69, 69, 69, 69, 69, 69, 42, 42, 42, 42, 42, 4, 1, 1, 1, 69, 69, 69] 74
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33])
total number of confs: 213
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078850 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078850
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078850/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078850
Building REAL300000078851
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078851'
/scratch/stefan/7769659/working/building/REAL300000078851 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078851

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078851/0 /scratch/stefan/7769659/working/building/REAL300000078851 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/886
`/scratch/stefan/7769659/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(F)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000078851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078851 none COC1=CC(C=NNC2=CC=CC(F)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [62, 37, 37, 37, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 89, 110, 110, 110, 62, 62, 62, 37, 15, 4, 1, 1, 1, 37, 110, 110] 110
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37])
total number of confs: 289
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078851 none COC1=CC(C=NNC2=CC=CC(F)=N2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 24, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 1, 1, 1, 9, 17, 25, 25, 3, 3, 3, 1, 7, 24, 37, 37, 37, 1, 17, 17] 110
rigid atoms, others: [1, 2, 3, 4, 5, 35, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 172
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078851 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078851
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078851/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078851
Building REAL300000078852
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078852'
/scratch/stefan/7769659/working/building/REAL300000078852 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078852

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078852/0 /scratch/stefan/7769659/working/building/REAL300000078852 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/887
`/scratch/stefan/7769659/working/3D/887' -> `0.mol2'
Preparing input files

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

`REAL300000078852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078852 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [23, 21, 23, 29, 29, 29, 21, 21, 15, 21, 21, 21, 21, 21, 21, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 29, 29, 21, 21, 21, 14, 4, 1, 1, 1] 29
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 103
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078852 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 4, 12, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 21, 21, 21, 21, 21, 21, 4, 4, 4, 12, 12, 1, 1, 1, 5, 16, 21, 21, 21] 29
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 106
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078852 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078852/1 /scratch/stefan/7769659/working/building/REAL300000078852 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/888
`/scratch/stefan/7769659/working/3D/888' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CC=CC(F)=N1)

`REAL300000078852.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078852/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078852 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [145, 105, 145, 201, 201, 201, 105, 105, 105, 105, 105, 105, 105, 105, 105, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 201, 201, 105, 105, 105, 42, 43, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 649
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078852 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 15, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 50, 51, 105, 105, 105, 105, 105, 105, 4, 4, 4, 15, 15, 1, 1, 1, 8, 8, 105, 105, 105] 201
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 248
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078852 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078852
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078852/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078852/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078852
Building REAL300000078853
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078853'
/scratch/stefan/7769659/working/building/REAL300000078853 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078853

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078853/0 /scratch/stefan/7769659/working/building/REAL300000078853 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/889
`/scratch/stefan/7769659/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000078853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 36, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 9, 19, 19, 15, 19, 19, 19, 19, 19, 1, 1, 7, 7, 7, 36, 57, 57, 57, 1, 1, 19, 19, 19, 19, 1, 1] 174
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 171
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 20, 57, 57, 34, 57, 155, 174, 174, 174, 174, 174, 174, 174, 174, 57, 57, 20, 20, 20, 4, 1, 1, 1, 57, 57, 174, 174, 174, 174, 57, 57] 174
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 352
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(=NNC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [80, 19, 80, 80, 171, 174, 174, 174, 174, 174, 174, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 80, 80, 80, 171, 174, 174, 174, 19, 19, 1, 1, 1, 1, 19, 19] 174
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 466
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078853 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078853/1 /scratch/stefan/7769659/working/building/REAL300000078853 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/890
`/scratch/stefan/7769659/working/3D/890' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1)

`REAL300000078853.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078853/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 31, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 7, 7, 7, 7, 59, 59, 59, 1, 1, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [1, 34, 35, 40, 41, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 59, 59, 36, 37, 182, 201, 201, 201, 201, 201, 201, 201, 201, 59, 59, 27, 27, 27, 27, 1, 1, 1, 59, 59, 201, 201, 201, 201, 59, 59] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078853 none CC(N=NC1=CC=CC(F)=N1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 49, 159, 159, 201, 201, 201, 201, 201, 201, 5, 18, 18, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 18, 18, 49, 49, 49, 49, 201, 201, 201, 18, 18, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 429
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078853 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078853
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078853/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078853/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078853
Building REAL300000078854
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078854'
/scratch/stefan/7769659/working/building/REAL300000078854 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078854

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078854/0 /scratch/stefan/7769659/working/building/REAL300000078854 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/891
`/scratch/stefan/7769659/working/3D/891' -> `0.mol2'
Preparing input files

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

`REAL300000078854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078854 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 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: [69, 40, 40, 40, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 120, 188, 195, 201, 197, 69, 69, 69, 40, 14, 4, 1, 1, 1, 40, 40, 188, 188, 195, 195] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 593
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078854 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 27, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 9, 46, 58, 86, 66, 4, 4, 4, 1, 9, 27, 40, 40, 40, 1, 1, 46, 46, 58, 58] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 414
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078854 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078854/1 /scratch/stefan/7769659/working/building/REAL300000078854 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/892
`/scratch/stefan/7769659/working/3D/892' -> `1.mol2'
Preparing input files

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

`REAL300000078854.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078854/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078854 none COC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [91, 51, 51, 51, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 152, 189, 189, 201, 195, 91, 91, 91, 51, 13, 14, 1, 1, 1, 51, 51, 189, 189, 189, 189] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 564
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078854 none COC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 44, 44, 51, 51, 50, 51, 51, 51, 1, 1, 1, 1, 9, 14, 14, 24, 22, 3, 3, 3, 1, 6, 6, 51, 51, 50, 1, 1, 14, 14, 14, 14] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 15, 16, 17, 18, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078854 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078854
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078854/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078854/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078854
Building REAL300000078855
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078855'
/scratch/stefan/7769659/working/building/REAL300000078855 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078855

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078855/0 /scratch/stefan/7769659/working/building/REAL300000078855 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/893
`/scratch/stefan/7769659/working/3D/893' -> `0.mol2'
Preparing input files

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

`REAL300000078855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078855 none CC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 39, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 39, 43, 43, 43, 1, 2, 2, 2, 2, 2, 2] 43
rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 121
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078855 none CC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 4, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 43
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 63
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078855 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078855
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078855/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078855
Building REAL300000078856
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078856'
/scratch/stefan/7769659/working/building/REAL300000078856 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078856

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078856/0 /scratch/stefan/7769659/working/building/REAL300000078856 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/894
`/scratch/stefan/7769659/working/3D/894' -> `0.mol2'
Preparing input files

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

`REAL300000078856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078856 none CC(OC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
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: [113, 89, 17, 17, 51, 51, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 113, 116, 116, 113, 113, 113, 113, 51, 51, 17, 4, 1, 1, 1, 51, 51] 116
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 369
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078856 none CC(OC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 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]
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: [20, 7, 1, 1, 1, 1, 1, 1, 8, 8, 33, 51, 51, 51, 51, 51, 51, 1, 1, 20, 28, 28, 20, 20, 20, 20, 1, 1, 8, 33, 51, 51, 51, 1, 1] 116
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 18, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 203
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078856 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078856/1 /scratch/stefan/7769659/working/building/REAL300000078856 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/895
`/scratch/stefan/7769659/working/3D/895' -> `1.mol2'
Preparing input files

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

`REAL300000078856.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078856/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078856 none CC(OC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 148, 83, 20, 84, 84, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 84, 84, 20, 20, 1, 1, 1, 84, 84] 201
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 735
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078856 none CC(OC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 8, 51, 51, 84, 84, 84, 84, 84, 84, 1, 1, 14, 19, 19, 14, 14, 14, 14, 1, 1, 8, 8, 84, 84, 84, 1, 1] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 18, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32])
total number of confs: 200
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078856 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078856
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078856/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078856/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078856
Building REAL300000078857
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078857'
/scratch/stefan/7769659/working/building/REAL300000078857 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078857

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078857/0 /scratch/stefan/7769659/working/building/REAL300000078857 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/896
`/scratch/stefan/7769659/working/3D/896' -> `0.mol2'
Preparing input files

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

`REAL300000078857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078857 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 111, 111, 111, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 201, 201, 111, 32, 33, 1, 1, 1, 111, 111, 111, 111] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 657
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078857 none O=C([O-])CN1C=C(CN=NC2=CC=CC(F)=N2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 8, 12, 1, 1, 1, 1, 1, 8, 61, 61, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 111, 111, 111, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078857 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078857
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078857/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078857
Building REAL300000078858
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078858'
/scratch/stefan/7769659/working/building/REAL300000078858 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078858

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078858/0 /scratch/stefan/7769659/working/building/REAL300000078858 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/897
`/scratch/stefan/7769659/working/3D/897' -> `0.mol2'
Preparing input files

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

`REAL300000078858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078858 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 7, 21, 35, 51, 73, 73, 1, 11, 11, 11, 29, 29, 29, 29, 1, 1, 1, 21, 21, 35, 35, 51, 51, 1] 201
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 16, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 376
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078858 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 85, 127, 160, 201, 201, 201, 29, 6, 6, 6, 2, 1, 1, 1, 29, 29, 29, 127, 127, 160, 160, 201, 201, 29] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 721
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078858 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078858/1 /scratch/stefan/7769659/working/building/REAL300000078858 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/898
`/scratch/stefan/7769659/working/3D/898' -> `1.mol2'
Preparing input files

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

`REAL300000078858.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078858/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078858 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 20, 20, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 6, 22, 28, 47, 64, 64, 1, 5, 5, 5, 5, 30, 30, 30, 1, 1, 1, 22, 22, 28, 28, 47, 47, 1] 201
rigid atoms, others: [32, 1, 33, 40, 11, 12, 13, 14, 15, 16, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39])
total number of confs: 324
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078858 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 30, 30, 111, 156, 163, 201, 201, 201, 30, 10, 10, 10, 10, 1, 1, 1, 30, 30, 30, 156, 156, 163, 163, 201, 201, 30] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 645
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078858 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078858
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078858/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078858/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078858
Building REAL300000078859
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078859'
/scratch/stefan/7769659/working/building/REAL300000078859 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078859

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078859/0 /scratch/stefan/7769659/working/building/REAL300000078859 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/899
`/scratch/stefan/7769659/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1)

`REAL300000078859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078859 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 28, 60, 65, 65, 65, 65, 65, 175, 201, 201, 201, 201, 65, 65, 7, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 62, 62, 64, 65, 65, 65, 201, 201, 201, 201, 65, 65, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 567
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078859 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 2, 1, 1, 1, 1, 1, 1, 11, 27, 27, 39, 39, 1, 1, 8, 35, 35, 65, 65, 65, 65, 65, 65, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 65, 65, 65] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43])
total number of confs: 237
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078859 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078859
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078859/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078859
Building REAL300000078860
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078860'
/scratch/stefan/7769659/working/building/REAL300000078860 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078860

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078860/0 /scratch/stefan/7769659/working/building/REAL300000078860 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/900
`/scratch/stefan/7769659/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1)

`REAL300000078860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078860 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 28, 59, 63, 63, 63, 63, 63, 146, 201, 201, 201, 63, 63, 7, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 62, 62, 62, 63, 63, 63, 201, 201, 63, 63, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 670
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078860 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 3, 2, 1, 1, 1, 1, 1, 1, 6, 22, 38, 38, 1, 1, 8, 37, 37, 63, 63, 63, 63, 63, 63, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 22, 22, 1, 1, 63, 63, 63] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40])
total number of confs: 229
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078860 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078860
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078860/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078860
Building REAL300000078861
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078861'
/scratch/stefan/7769659/working/building/REAL300000078861 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078861

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078861/0 /scratch/stefan/7769659/working/building/REAL300000078861 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/901
`/scratch/stefan/7769659/working/3D/901' -> `0.mol2'
Preparing input files

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

`REAL300000078861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078861 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 11, 11, 11, 39, 51, 51, 51, 1, 1, 1, 30, 30, 30, 30, 1] 201
rigid atoms, others: [32, 1, 37, 11, 12, 13, 14, 15, 16, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 270
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078861 none CC(=NNC1=CC=CC(F)=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 51, 51, 51, 51, 51, 153, 201, 201, 201, 201, 51, 13, 13, 13, 4, 1, 1, 1, 51, 51, 51, 201, 201, 201, 201, 51] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 481
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078861 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078861/1 /scratch/stefan/7769659/working/building/REAL300000078861 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/902
`/scratch/stefan/7769659/working/3D/902' -> `1.mol2'
Preparing input files

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

`REAL300000078861.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078861/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078861 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 11, 27, 27, 37, 37, 1, 7, 7, 7, 7, 49, 49, 49, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [32, 1, 37, 11, 12, 13, 14, 15, 16, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 204
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078861 none CC(N=NC1=CC=CC(F)=N1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 49, 49, 49, 49, 49, 159, 201, 201, 201, 201, 49, 17, 17, 17, 17, 1, 1, 1, 49, 49, 49, 201, 201, 201, 201, 49] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 472
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078861 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078861
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078861/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078861/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078861
Building REAL300000078862
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078862'
/scratch/stefan/7769659/working/building/REAL300000078862 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078862

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078862/0 /scratch/stefan/7769659/working/building/REAL300000078862 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/903
`/scratch/stefan/7769659/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1)

`REAL300000078862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078862 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 7, 30, 60, 69, 69, 69, 69, 69, 193, 201, 201, 201, 198, 69, 69, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 67, 67, 67, 69, 69, 69, 201, 201, 201, 201, 69, 69, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 515
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078862 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 23, 23, 1, 1, 9, 41, 41, 69, 69, 69, 69, 69, 69, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 1, 1, 69, 69, 69] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 14, 15, 40, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43])
total number of confs: 194
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078862 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078862
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078862/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078862
Building REAL300000078863
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078863'
/scratch/stefan/7769659/working/building/REAL300000078863 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078863

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078863/0 /scratch/stefan/7769659/working/building/REAL300000078863 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/904
`/scratch/stefan/7769659/working/3D/904' -> `0.mol2'
Preparing input files

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

`REAL300000078863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078863 none CCC(=NNC1=CC=CC(F)=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 7, 7, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 10, 24, 30, 49, 54, 57, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 1, 1, 10, 10, 23, 23, 30, 30, 49, 49, 1, 1] 201
rigid atoms, others: [2, 35, 36, 45, 12, 13, 14, 15, 16, 46, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 328
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078863 none CCC(=NNC1=CC=CC(F)=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 78, 90, 133, 144, 193, 194, 197, 23, 23, 11, 11, 11, 11, 11, 2, 1, 1, 1, 23, 23, 90, 90, 133, 133, 144, 144, 193, 193, 23, 23] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 762
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078863 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078863/1 /scratch/stefan/7769659/working/building/REAL300000078863 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/905
`/scratch/stefan/7769659/working/3D/905' -> `1.mol2'
Preparing input files

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

`REAL300000078863.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078863/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078863 none CCC(N=NC1=CC=CC(F)=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 1, 4, 11, 11, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 6, 10, 25, 31, 50, 55, 59, 1, 1, 5, 5, 5, 5, 5, 4, 21, 21, 21, 1, 1, 10, 10, 24, 24, 32, 32, 49, 49, 1, 1] 201
rigid atoms, others: [2, 35, 36, 45, 12, 13, 14, 15, 16, 46, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078863 none CCC(N=NC1=CC=CC(F)=N1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 13, 21, 21, 13, 20, 78, 93, 139, 147, 194, 199, 201, 21, 21, 19, 19, 19, 19, 19, 13, 1, 1, 1, 21, 21, 93, 93, 139, 139, 147, 147, 194, 194, 21, 21] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 835
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078863 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078863
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078863/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078863/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078863
Building REAL300000078864
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078864'
/scratch/stefan/7769659/working/building/REAL300000078864 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078864

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078864/0 /scratch/stefan/7769659/working/building/REAL300000078864 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/906
`/scratch/stefan/7769659/working/3D/906' -> `0.mol2'
Preparing input files

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

`REAL300000078864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078864 none COC1=CC(C(C)=NNC2=CC=CC(F)=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 30, 30, 30, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 104, 174, 182, 201, 201, 201, 49, 49, 49, 30, 7, 7, 7, 2, 1, 1, 1, 30, 30, 174, 174, 182, 182, 201, 201] 201
rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 656
number of broken/clashed sets: 129
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078864 none COC1=CC(C(C)=NNC2=CC=CC(F)=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 9, 28, 34, 45, 58, 58, 3, 3, 3, 1, 11, 11, 11, 30, 30, 30, 30, 1, 1, 28, 28, 34, 34, 45, 45] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 323
number of broken/clashed sets: 129
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078864 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078864/1 /scratch/stefan/7769659/working/building/REAL300000078864 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/907
`/scratch/stefan/7769659/working/3D/907' -> `1.mol2'
Preparing input files

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

`REAL300000078864.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078864/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078864 none COC1=CC(C(C)N=NC2=CC=CC(F)=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 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: [71, 45, 45, 45, 14, 4, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 116, 177, 180, 201, 201, 201, 71, 71, 71, 45, 14, 14, 14, 14, 1, 1, 1, 45, 45, 177, 177, 180, 180, 201, 201] 201
rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 679
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078864 none COC1=CC(C(C)N=NC2=CC=CC(F)=N2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 25, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 7, 15, 17, 27, 33, 33, 3, 3, 3, 1, 7, 7, 7, 7, 45, 45, 45, 1, 1, 15, 15, 17, 17, 27, 27] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078864 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078864
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078864/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078864/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078864
Building REAL300000078865
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078865'
/scratch/stefan/7769659/working/building/REAL300000078865 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078865

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078865/0 /scratch/stefan/7769659/working/building/REAL300000078865 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/908
`/scratch/stefan/7769659/working/3D/908' -> `0.mol2'
Preparing input files

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

`REAL300000078865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078865 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5] 16
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 32
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078865 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 1, 1] 16
rigid atoms, others: [1, 34, 3, 4, 33, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 20
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078865 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 8, 8, 8, 1, 1, 1, 8, 8] 16
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 30
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078865 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078865
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078865/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078865
Building REAL300000078866
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078866'
/scratch/stefan/7769659/working/building/REAL300000078866 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078866

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078866/0 /scratch/stefan/7769659/working/building/REAL300000078866 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/909
`/scratch/stefan/7769659/working/3D/909' -> `0.mol2'
Preparing input files

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

`REAL300000078866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078866 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [8, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 6, 6] 16
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 33
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078866 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 6, 6, 6, 6, 1, 1, 1, 7, 7, 7, 1, 1] 16
rigid atoms, others: [1, 34, 3, 4, 33, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32])
total number of confs: 20
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078866 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC(F)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [8, 7, 8, 7, 7, 16, 16, 16, 16, 16, 16, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 7, 7, 7, 1, 1, 1, 7, 7] 16
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 34
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078866 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078866
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078866/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078866
Building REAL300000078867
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078867'
/scratch/stefan/7769659/working/building/REAL300000078867 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078867

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078867/0 /scratch/stefan/7769659/working/building/REAL300000078867 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/910
`/scratch/stefan/7769659/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078867 none CC(N=NC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 32, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 56, 56, 7, 7, 7, 7, 58, 58, 58, 1, 1, 1, 33, 33] 201
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 273
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078867 none CC(N=NC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 58, 58, 58, 32, 58, 58, 58, 143, 201, 201, 201, 27, 27, 27, 27, 1, 1, 1, 58, 58, 58, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078867 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078867/1 /scratch/stefan/7769659/working/building/REAL300000078867 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/911
`/scratch/stefan/7769659/working/3D/911' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078867.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078867/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078867 none CC(=NNC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 47, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 74, 74, 11, 11, 11, 47, 68, 68, 68, 1, 1, 1, 43, 43] 201
rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 384
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078867 none CC(=NNC1=CC=CC(F)=N1)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 68, 68, 68, 18, 68, 68, 68, 153, 201, 201, 201, 18, 18, 18, 4, 1, 1, 1, 68, 68, 68, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 643
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078867 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078867
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078867/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078867/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078867
Building REAL300000078868
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078868'
/scratch/stefan/7769659/working/building/REAL300000078868 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078868

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078868/0 /scratch/stefan/7769659/working/building/REAL300000078868 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/912
`/scratch/stefan/7769659/working/3D/912' -> `0.mol2'
Preparing input files

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

`REAL300000078868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078868 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(F)=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 34, 8, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 80, 80, 80, 63, 63, 63, 63, 63, 63, 34, 34, 34, 34, 1, 1, 1, 80, 80] 80
rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078868 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(F)=N1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 6, 6, 38, 38, 63, 63, 63, 63, 63, 63, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6, 63, 63, 63, 2, 2] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078868 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078868/1 /scratch/stefan/7769659/working/building/REAL300000078868 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/913
`/scratch/stefan/7769659/working/3D/913' -> `1.mol2'
Preparing input files

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

`REAL300000078868.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078868/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078868 none CC(=NNC1=CC=CC(F)=N1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 40, 45, 45, 45, 45, 45, 45, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 45, 45, 45, 2, 2, 1, 1, 2, 2, 2, 1] 45
rigid atoms, others: [1, 34, 35, 39, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 141
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078868 none CC(=NNC1=CC=CC(F)=N1)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 17, 4, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45] 45
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 64
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078868 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078868
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078868/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078868/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078868
Building REAL300000078869
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078869'
/scratch/stefan/7769659/working/building/REAL300000078869 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078869

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078869/0 /scratch/stefan/7769659/working/building/REAL300000078869 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/914
`/scratch/stefan/7769659/working/3D/914' -> `0.mol2'
Preparing input files

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

`REAL300000078869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078869 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1] 7
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 12
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078869 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6] 7
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078869 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078869/1 /scratch/stefan/7769659/working/building/REAL300000078869 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/915
`/scratch/stefan/7769659/working/3D/915' -> `1.mol2'
Preparing input files

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

`REAL300000078869.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078869/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078869 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 14
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078869 none O=C([O-])C1=CC=C2C(=C1)CCCCC2N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22])
total number of confs: 12
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078869 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078869
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078869/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078869/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078869
Building REAL300000078870
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078870'
/scratch/stefan/7769659/working/building/REAL300000078870 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078870

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078870/0 /scratch/stefan/7769659/working/building/REAL300000078870 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/916
`/scratch/stefan/7769659/working/3D/916' -> `0.mol2'
Preparing input files

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

`REAL300000078870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 94, 25, 25, 25, 25, 25, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 25, 193, 201, 201, 193, 201, 201, 193, 25, 25, 25, 9, 3, 1, 1, 1, 25, 201, 201, 193, 201, 201] 201
rigid atoms, others: [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, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 644
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 50, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 25, 25, 1, 34, 48, 48, 34, 48, 48, 34, 1, 1, 1, 6, 23, 25, 25, 25, 1, 48, 48, 34, 48, 48] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 36, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 306
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 3, 10, 48, 48, 48, 48, 48, 142, 142, 199, 201, 201, 201, 201, 201, 201, 48, 1, 1, 1, 1, 1, 1, 3, 48, 48, 48, 142, 199, 201, 201, 201, 48, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 37, 38, 39, 40, 41, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 523
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078870 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078870/1 /scratch/stefan/7769659/working/building/REAL300000078870 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/917
`/scratch/stefan/7769659/working/3D/917' -> `1.mol2'
Preparing input files

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

`REAL300000078870.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078870/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 115, 40, 40, 40, 40, 40, 15, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 14, 15, 1, 1, 1, 40, 201, 201, 201, 201, 201] 201
rigid atoms, others: [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, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 600
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 21, 25, 9, 1, 1, 1, 1, 1, 1, 1, 6, 34, 35, 40, 40, 40, 40, 40, 40, 1, 21, 28, 28, 21, 28, 28, 21, 1, 1, 1, 6, 6, 40, 40, 40, 1, 28, 28, 21, 28, 28] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 36, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078870 none O=C([O-])C(OC1=CC=CC(CN=NC2=CC=CC(F)=N2)=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 4, 1, 3, 7, 28, 28, 8, 28, 28, 103, 198, 198, 201, 201, 201, 201, 201, 201, 28, 1, 1, 1, 1, 1, 1, 3, 28, 28, 13, 103, 103, 201, 201, 201, 28, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 37, 38, 39, 40, 41, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 528
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078870 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078870
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078870/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078870/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078870
Building REAL300000078871
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078871'
/scratch/stefan/7769659/working/building/REAL300000078871 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078871

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078871/0 /scratch/stefan/7769659/working/building/REAL300000078871 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/918
`/scratch/stefan/7769659/working/3D/918' -> `0.mol2'
Preparing input files

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

`REAL300000078871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078871 none CC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 51, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 21, 21, 11, 11, 11, 51, 73, 73, 73, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 93
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 226
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078871 none CC(=NNC1=CC=CC(F)=N1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 73, 73, 73, 73, 73, 73, 73, 73, 73, 93, 93, 93, 16, 16, 16, 4, 1, 1, 1, 73, 73, 73, 93, 93, 93, 93, 93, 93, 93] 93
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 136
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078871 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078871/1 /scratch/stefan/7769659/working/building/REAL300000078871 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/919
`/scratch/stefan/7769659/working/3D/919' -> `1.mol2'
Preparing input files

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

`REAL300000078871.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078871/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078871 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 119, 80, 80, 80, 80, 80, 80, 80, 80, 80, 35, 8, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 80, 80, 80, 35, 35, 35, 35, 1, 1, 1] 119
rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 248
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078871 none CC(C)OC1=CC=C(C(=O)[O-])C=C1C(C)N=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [14, 8, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 45, 45, 80, 80, 80, 80, 80, 80, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 80, 80, 80] 119
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 11, 12, 13, 31] set([0, 1, 2, 9, 10, 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: 172
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078871 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078871
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078871/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078871/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078871
Building REAL300000078872
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078872'
/scratch/stefan/7769659/working/building/REAL300000078872 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078872

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078872/0 /scratch/stefan/7769659/working/building/REAL300000078872 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/920
`/scratch/stefan/7769659/working/3D/920' -> `0.mol2'
Preparing input files

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

`REAL300000078872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 33, 34, 50, 50, 50, 50, 50, 50, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 50, 50, 50, 1, 1, 3, 3] 76
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 56, 56, 76, 76, 76, 76, 76, 76, 3, 3, 1, 1, 1, 1, 3, 3, 12, 12, 76, 76, 76, 3, 3, 1, 1] 76
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: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 49, 76, 49, 76, 76, 30, 30, 49, 49, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 76, 76, 76, 76, 49, 49, 30, 30, 1, 1, 1, 49, 49, 76, 76] 76
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 435
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078872 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078872/1 /scratch/stefan/7769659/working/building/REAL300000078872 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/921
`/scratch/stefan/7769659/working/3D/921' -> `1.mol2'
Preparing input files

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

`REAL300000078872.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078872/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 3, 1, 1, 4, 7, 12, 12, 12, 1, 1, 3, 3] 13
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 32
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 3, 2, 1, 7, 8, 11, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 13, 13, 13, 3, 3, 1, 1] 13
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: 44
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078872 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 13, 12, 12, 12, 4, 1, 1, 1, 12, 12, 13, 13] 13
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 22
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078872 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078872
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078872/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078872/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078872
Building REAL300000078873
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078873'
/scratch/stefan/7769659/working/building/REAL300000078873 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078873

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078873/0 /scratch/stefan/7769659/working/building/REAL300000078873 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/922
`/scratch/stefan/7769659/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(F)=N2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000078873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078873 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [67, 43, 43, 43, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 77, 100, 100, 106, 106, 67, 67, 67, 43, 16, 4, 1, 1, 1, 43, 100, 100, 100, 100] 106
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38])
total number of confs: 293
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078873 none COC1=CC(C=NNC2=CC=CC(F)=N2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 8, 8, 30, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 5, 13, 13, 21, 21, 4, 4, 4, 1, 8, 30, 43, 43, 43, 1, 13, 14, 14, 14] 106
rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 180
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078873 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078873
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078873/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078873
Building REAL300000078874
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078874'
/scratch/stefan/7769659/working/building/REAL300000078874 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078874

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078874/0 /scratch/stefan/7769659/working/building/REAL300000078874 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/923
`/scratch/stefan/7769659/working/3D/923' -> `0.mol2'
Preparing input files

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

`REAL300000078874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
206  conformations in input
total number of sets (complete confs): 206
using faster count positions algorithm for large data
unique positions, atoms: [25, 12, 25, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 26, 34, 34, 34, 34, 34, 34, 1, 12, 12, 12, 12, 12, 1, 1, 9, 26, 34, 34, 34, 12, 12, 24] 206
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 164
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
206  conformations in input
total number of sets (complete confs): 206
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 55, 55, 101, 103, 103, 103, 103, 103, 103, 12, 1, 1, 1, 1, 1, 12, 12, 55, 101, 103, 103, 103, 1, 1, 2] 206
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
206  conformations in input
total number of sets (complete confs): 206
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 103, 103, 34, 34, 34, 34, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 34, 103, 103, 103, 103, 103, 34, 34, 17, 4, 1, 1, 1, 103, 103, 206] 206
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 346
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078874 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078874/1 /scratch/stefan/7769659/working/building/REAL300000078874 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/924
`/scratch/stefan/7769659/working/3D/924' -> `1.mol2'
Preparing input files

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

`REAL300000078874.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078874/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 15, 12, 12, 1, 1, 1, 1, 1, 1, 8, 69, 69, 113, 113, 113, 113, 113, 113, 1, 12, 12, 11, 11, 12, 1, 1, 8, 8, 113, 113, 113, 12, 12, 24] 402
rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 61, 176, 176, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 61, 61, 201, 201, 201, 1, 1, 2] 402
rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078874 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)O2)=CC=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 113, 113, 113, 113, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 113, 113, 23, 23, 1, 1, 1, 201, 201, 402] 402
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 717
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078874 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078874
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078874/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078874/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078874
Building REAL300000078875
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078875'
/scratch/stefan/7769659/working/building/REAL300000078875 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078875

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078875/0 /scratch/stefan/7769659/working/building/REAL300000078875 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/925
`/scratch/stefan/7769659/working/3D/925' -> `0.mol2'
Preparing input files

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

`REAL300000078875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078875 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1] 6
rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 10
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078875 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 6, 6, 6, 6] 6
rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078875 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078875
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078875/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078875
Building REAL300000078876
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078876'
/scratch/stefan/7769659/working/building/REAL300000078876 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078876

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078876/0 /scratch/stefan/7769659/working/building/REAL300000078876 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/926
`/scratch/stefan/7769659/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)C=C1)

`REAL300000078876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078876 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [7, 4, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 14, 14, 14, 14, 14, 14, 1, 6, 6, 6, 6, 1, 1, 6, 13, 14, 14, 14, 6, 6] 32
rigid atoms, others: [6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078876 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 8, 8, 8, 27, 27, 30, 30, 30, 30, 30, 30, 30, 8, 1, 1, 1, 1, 8, 8, 26, 29, 30, 30, 30, 1, 1] 30
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: 75
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078876 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 18, 32, 32, 14, 14, 14, 14, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 32, 32, 32, 32, 14, 14, 9, 4, 1, 1, 1, 32, 32] 32
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 104
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078876 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078876
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078876/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078876
Building REAL300000078877
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078877'
/scratch/stefan/7769659/working/building/REAL300000078877 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078877

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078877/0 /scratch/stefan/7769659/working/building/REAL300000078877 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/927
`/scratch/stefan/7769659/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)=C1)

`REAL300000078877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 31, 41, 41, 41, 41, 41, 41, 1, 13, 12, 13, 13, 1, 1, 7, 31, 41, 41, 41, 13] 69
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 46, 46, 69, 69, 69, 69, 69, 69, 69, 13, 1, 1, 1, 1, 13, 13, 46, 69, 69, 69, 69, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 69, 69, 69, 69, 69, 69, 41, 41, 41, 41, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 69, 69, 69, 69, 41, 41, 16, 4, 1, 1, 1, 69] 69
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 106
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078877 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078877/1 /scratch/stefan/7769659/working/building/REAL300000078877 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/928
`/scratch/stefan/7769659/working/3D/928' -> `1.mol2'
Preparing input files

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

`REAL300000078877.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078877/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 9, 64, 64, 95, 95, 95, 95, 95, 95, 1, 12, 12, 12, 12, 1, 1, 9, 9, 95, 95, 95, 12] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 12, 12, 12, 12, 61, 181, 181, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 61, 61, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 397
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078877 none O=C([O-])C1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 95, 95, 24, 25, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 330
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078877 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078877
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078877/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078877/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078877
Building REAL300000078878
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078878'
/scratch/stefan/7769659/working/building/REAL300000078878 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078878

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078878/0 /scratch/stefan/7769659/working/building/REAL300000078878 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/929
`/scratch/stefan/7769659/working/3D/929' -> `0.mol2'
Preparing input files

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

`REAL300000078878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078878 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(F)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 11, 5, 1, 1, 1, 13] 13
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078878 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(F)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 6, 12, 13, 13, 13, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078878 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078878
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078878/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078878
Building REAL300000078879
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078879'
/scratch/stefan/7769659/working/building/REAL300000078879 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078879

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078879/0 /scratch/stefan/7769659/working/building/REAL300000078879 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/930
`/scratch/stefan/7769659/working/3D/930' -> `0.mol2'
Preparing input files

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

`REAL300000078879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078879 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC(F)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 5] 5
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 9
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078879 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC(F)=N3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1] 5
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33] set([32, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31])
total number of confs: 11
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078879 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078879
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078879/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078879
Building REAL300000078880
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078880'
/scratch/stefan/7769659/working/building/REAL300000078880 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078880

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078880/0 /scratch/stefan/7769659/working/building/REAL300000078880 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/931
`/scratch/stefan/7769659/working/3D/931' -> `0.mol2'
Preparing input files

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

`REAL300000078880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078880 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 12, 4, 1, 1, 1, 16] 16
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27])
total number of confs: 27
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078880 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 10, 10, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 10, 16, 16, 16, 16, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078880 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078880
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078880/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078880
Building REAL300000078881
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078881'
/scratch/stefan/7769659/working/building/REAL300000078881 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078881

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078881/0 /scratch/stefan/7769659/working/building/REAL300000078881 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/932
`/scratch/stefan/7769659/working/3D/932' -> `0.mol2'
Preparing input files

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

`REAL300000078881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078881 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 7, 3, 1, 1, 1, 11] 22
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 28])
total number of confs: 40
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078881 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 11, 1, 1, 2, 8, 11, 11, 11, 11, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 31
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078881 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078881/1 /scratch/stefan/7769659/working/building/REAL300000078881 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/933
`/scratch/stefan/7769659/working/3D/933' -> `1.mol2'
Preparing input files

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

`REAL300000078881.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078881/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078881 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 1, 1, 1, 6] 6
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 27])
total number of confs: 10
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078881 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 6, 6, 6, 6, 6, 6, 6, 1, 1, 4, 6, 6, 6, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26])
total number of confs: 17
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078881 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078881
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078881/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078881/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078881
Building REAL300000078882
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078882'
/scratch/stefan/7769659/working/building/REAL300000078882 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078882

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078882/0 /scratch/stefan/7769659/working/building/REAL300000078882 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/934
`/scratch/stefan/7769659/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=CC(F)=N2)=C1OCC(=O)[O-])

`REAL300000078882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078882 none COC1=CC(Br)=CC(C=NNC2=CC=CC(F)=N2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [25, 15, 15, 15, 15, 15, 15, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 24, 34, 36, 36, 25, 25, 25, 15, 15, 10, 4, 1, 1, 1, 34, 34] 36
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 120
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078882 none COC1=CC(Br)=CC(C=NNC2=CC=CC(F)=N2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 15, 15, 15, 15, 15, 15, 1, 1, 3, 11, 19, 19, 4, 4, 4, 1, 1, 4, 10, 15, 15, 15, 11, 11] 36
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 105
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078882 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078882/1 /scratch/stefan/7769659/working/building/REAL300000078882 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/935
`/scratch/stefan/7769659/working/3D/935' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(CN=NC2=CC=CC(F)=N2)=C1OCC(=O)[O-])

`REAL300000078882.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078882/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078882 none COC1=CC(Br)=CC(CN=NC2=CC=CC(F)=N2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [145, 87, 87, 87, 87, 87, 87, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 133, 197, 201, 201, 145, 145, 145, 87, 87, 34, 34, 1, 1, 1, 197, 197] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 759
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078882 none COC1=CC(Br)=CC(CN=NC2=CC=CC(F)=N2)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 47, 48, 87, 87, 87, 87, 87, 87, 1, 1, 2, 12, 25, 25, 3, 3, 3, 1, 1, 8, 8, 87, 87, 87, 12, 12] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 229
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078882 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078882
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078882/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078882/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078882
Building REAL300000078883
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078883'
/scratch/stefan/7769659/working/building/REAL300000078883 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078883

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078883/0 /scratch/stefan/7769659/working/building/REAL300000078883 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/936
`/scratch/stefan/7769659/working/3D/936' -> `0.mol2'
Preparing input files

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

`REAL300000078883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 8, 56, 56, 109, 109, 109, 109, 109, 109, 1, 1, 8, 8, 8, 2, 2, 1, 1, 8, 8, 109, 109, 109, 1, 1] 201
rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 8, 8, 7, 7, 38, 178, 178, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 7, 7, 8, 8, 38, 38, 201, 201, 201, 8, 8] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 108, 108, 24, 24, 108, 108, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 201, 201, 200, 108, 108, 108, 108, 24, 24, 1, 1, 1, 108, 108] 201
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 572
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078883 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078883/1 /scratch/stefan/7769659/working/building/REAL300000078883 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/937
`/scratch/stefan/7769659/working/3D/937' -> `1.mol2'
Preparing input files

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

`REAL300000078883.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078883/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [31, 30, 31, 30, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 39, 59, 59, 59, 59, 59, 59, 1, 1, 30, 30, 30, 7, 7, 1, 1, 11, 39, 59, 59, 59, 1, 1] 136
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 178
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 30, 30, 30, 30, 30, 105, 105, 133, 136, 136, 136, 136, 136, 136, 30, 30, 1, 1, 1, 8, 8, 30, 30, 105, 133, 136, 136, 136, 30, 30] 136
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 363
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078883 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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, 136, 136, 97, 59, 35, 33, 59, 59, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 136, 136, 136, 97, 97, 59, 59, 20, 4, 1, 1, 1, 59, 59] 136
rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38])
total number of confs: 414
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078883 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078883
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078883/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078883/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078883
Building REAL300000078884
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078884'
/scratch/stefan/7769659/working/building/REAL300000078884 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078884

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078884/0 /scratch/stefan/7769659/working/building/REAL300000078884 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/938
`/scratch/stefan/7769659/working/3D/938' -> `0.mol2'
Preparing input files

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

`REAL300000078884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078884 none O=C([O-])C1=CC(I)=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 6, 2, 1, 1, 1, 9] 9
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27])
total number of confs: 16
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078884 none O=C([O-])C1=CC(I)=CC(C=NNC2=CC=CC(F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 6, 8, 9, 9, 9, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078884 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078884
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078884/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078884
Building REAL300000078885
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078885'
/scratch/stefan/7769659/working/building/REAL300000078885 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078885

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078885/0 /scratch/stefan/7769659/working/building/REAL300000078885 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/939
`/scratch/stefan/7769659/working/3D/939' -> `0.mol2'
Preparing input files

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

`REAL300000078885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078885 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(F)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 14, 4, 1, 1, 1, 46] 46
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078885 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(F)=N2)=C1O NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 10, 20, 23, 23, 23, 2] 46
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078885 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078885
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078885/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078885
Building REAL300000078886
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078886'
/scratch/stefan/7769659/working/building/REAL300000078886 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078886

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078886/0 /scratch/stefan/7769659/working/building/REAL300000078886 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/940
`/scratch/stefan/7769659/working/3D/940' -> `0.mol2'
Preparing input files

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

`REAL300000078886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 56, 57, 93, 93, 93, 93, 93, 93, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 8, 93, 93, 93, 1, 1, 3] 201
rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 105, 105, 147, 147, 147, 147, 147, 147, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 17, 17, 147, 147, 147, 3, 3, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 40, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(CN=NC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 147, 147, 146, 147, 147, 42, 27, 92, 92, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 147, 201, 201, 147, 147, 147, 92, 92, 22, 22, 1, 1, 1, 92, 92, 147] 201
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 754
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078886 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078886/1 /scratch/stefan/7769659/working/building/REAL300000078886 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/941
`/scratch/stefan/7769659/working/3D/941' -> `1.mol2'
Preparing input files

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

`REAL300000078886.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078886/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 26, 27, 27, 27, 27, 27, 27, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 26, 27, 27, 27, 1, 1, 3] 67
rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 40])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 34, 35, 35, 35, 35, 35, 35, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 10, 30, 35, 35, 35, 3, 3, 1] 67
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 40, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078886 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(F)=N3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 35, 35, 35, 35, 26, 25, 27, 27, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 35, 67, 67, 35, 35, 35, 27, 27, 12, 4, 1, 1, 1, 27, 27, 35] 67
rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 264
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078886 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078886
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078886/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078886/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078886
Building REAL300000078887
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078887'
/scratch/stefan/7769659/working/building/REAL300000078887 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078887

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078887/0 /scratch/stefan/7769659/working/building/REAL300000078887 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/942
`/scratch/stefan/7769659/working/3D/942' -> `0.mol2'
Preparing input files

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

`REAL300000078887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078887 none CCOC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 51, 15, 15, 15, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 81, 165, 175, 175, 86, 86, 86, 86, 86, 15, 4, 2, 1, 1, 1, 15, 15, 165, 165] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078887 none CCOC1=CC(C=NNC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 7, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 39, 75, 75, 26, 26, 26, 26, 26, 1, 6, 14, 15, 15, 15, 1, 1, 39, 39] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 16, 17, 18, 35, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 375
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078887 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078887/1 /scratch/stefan/7769659/working/building/REAL300000078887 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/943
`/scratch/stefan/7769659/working/3D/943' -> `1.mol2'
Preparing input files

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

`REAL300000078887.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078887/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078887 none CCOC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 43, 43, 43, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 144, 197, 199, 199, 81, 81, 81, 81, 81, 43, 11, 12, 1, 1, 1, 43, 43, 197, 197] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 618
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078887 none CCOC1=CC(CN=NC2=CC=CC(F)=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 6, 40, 40, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 7, 19, 30, 30, 5, 5, 5, 5, 5, 1, 6, 6, 43, 43, 43, 1, 1, 19, 19] 201
rigid atoms, others: [19, 2, 3, 4, 5, 6, 16, 17, 18, 35, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078887 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078887
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078887/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078887/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078887
Building REAL300000078888
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078888'
/scratch/stefan/7769659/working/building/REAL300000078888 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078888

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078888/0 /scratch/stefan/7769659/working/building/REAL300000078888 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/944
`/scratch/stefan/7769659/working/3D/944' -> `0.mol2'
Preparing input files

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

`REAL300000078888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078888 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [13, 10, 13, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 32, 32, 32, 32] 32
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078888 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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
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, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 4, 12, 12, 12, 12] 32
rigid atoms, others: [1, 3, 4, 5, 6, 33, 12, 13, 14] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078888 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [13, 12, 13, 12, 12, 12, 12, 32, 32, 32, 32, 32, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 8, 2, 1, 1, 1] 32
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 74
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078888 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078888
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078888/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078888
Building REAL300000078889
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078889'
/scratch/stefan/7769659/working/building/REAL300000078889 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078889

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078889/0 /scratch/stefan/7769659/working/building/REAL300000078889 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/945
`/scratch/stefan/7769659/working/3D/945' -> `0.mol2'
Preparing input files

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

`REAL300000078889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078889 none COC1=CC=C(C)C(C=NNC2=CC=CC(F)=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 32, 32, 32, 32, 32, 32, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 38, 38, 38, 38, 38, 32, 32, 32, 32, 32, 20, 4, 1, 1, 1] 38
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078889 none COC1=CC=C(C)C(C=NNC2=CC=CC(F)=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 32, 32, 32, 32, 32, 32, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 7, 21, 32, 32, 32] 38
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078889 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078889
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078889/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078889
Building REAL300000078890
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078890'
/scratch/stefan/7769659/working/building/REAL300000078890 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078890

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078890/0 /scratch/stefan/7769659/working/building/REAL300000078890 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/946
`/scratch/stefan/7769659/working/3D/946' -> `0.mol2'
Preparing input files

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

`REAL300000078890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078890 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=CC(F)=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 1, 1, 1] 11
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078890 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=CC(F)=N2)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 4, 4, 10, 11, 11, 11, 11, 11, 11, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 10, 11, 11, 11] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078890 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078890
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078890/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078890
Building REAL300000078891
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078891'
/scratch/stefan/7769659/working/building/REAL300000078891 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078891

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078891/0 /scratch/stefan/7769659/working/building/REAL300000078891 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/947
`/scratch/stefan/7769659/working/3D/947' -> `0.mol2'
Preparing input files

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

`REAL300000078891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078891 none CC(=NNC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [9, 1, 9, 9, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 1, 1, 1, 1] 23
rigid atoms, others: [32, 1, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 65
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078891 none CC(=NNC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 4, 1, 1, 1, 23, 23, 23, 23] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 36
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078891 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078891/1 /scratch/stefan/7769659/working/building/REAL300000078891 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/948
`/scratch/stefan/7769659/working/3D/948' -> `1.mol2'
Preparing input files

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

`REAL300000078891.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078891/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078891 none CC(N=NC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 46, 46, 75, 75, 75, 75, 75, 75, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 75, 75, 75, 1, 1, 1, 1] 75
rigid atoms, others: [32, 1, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078891 none CC(N=NC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 30, 30, 30, 30, 1, 1, 1, 75, 75, 75, 75] 75
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078891 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078891
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078891/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078891/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078891
Building REAL300000078892
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078892'
/scratch/stefan/7769659/working/building/REAL300000078892 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078892

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078892/0 /scratch/stefan/7769659/working/building/REAL300000078892 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/949
`/scratch/stefan/7769659/working/3D/949' -> `0.mol2'
Preparing input files

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

`REAL300000078892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078892 none O=C([O-])C1=C(C=NNC2=CC=CC(F)=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 8, 4, 1, 1, 1, 12] 12
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 24])
total number of confs: 22
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078892 none O=C([O-])C1=C(C=NNC2=CC=CC(F)=N2)SC(Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 1, 1, 1, 5, 5, 11, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 5, 11, 12, 12, 12, 1] 12
rigid atoms, others: [1, 3, 4, 5, 15, 16, 17, 18, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078892 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078892
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078892/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078892
Building REAL300000078893
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078893'
/scratch/stefan/7769659/working/building/REAL300000078893 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078893

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078893/0 /scratch/stefan/7769659/working/building/REAL300000078893 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/950
`/scratch/stefan/7769659/working/3D/950' -> `0.mol2'
Preparing input files

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

`REAL300000078893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078893 none CC(=NNC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 1, 1, 1, 1, 1] 11
rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 31
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078893 none CC(=NNC1=CC=CC(F)=N1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 4, 1, 1, 1, 11, 11, 11, 11, 11] 11
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35])
total number of confs: 20
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078893 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078893
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078893/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078893
Building REAL300000078894
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078894'
/scratch/stefan/7769659/working/building/REAL300000078894 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078894

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078894/0 /scratch/stefan/7769659/working/building/REAL300000078894 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/951
`/scratch/stefan/7769659/working/3D/951' -> `0.mol2'
Preparing input files

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

`REAL300000078894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 31, 52, 52, 52, 52, 52, 52, 45, 45, 45, 16, 16, 1, 1, 1, 1, 7, 7, 52, 52, 52] 76
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 175
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 7, 31, 45, 45, 31, 45, 45, 45, 49, 68, 68, 76, 76, 76, 76, 76, 76, 1, 1, 1, 7, 7, 45, 45, 31, 45, 49, 49, 76, 76, 76] 76
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2CN=NC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 76, 71, 61, 52, 52, 52, 52, 52, 52, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 71, 71, 52, 52, 52, 52, 28, 28, 1, 1, 1] 76
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 211
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078894 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078894/1 /scratch/stefan/7769659/working/building/REAL300000078894 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/952
`/scratch/stefan/7769659/working/3D/952' -> `1.mol2'
Preparing input files

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

`REAL300000078894.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078894/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 141, 141, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 14, 141, 141, 141, 37, 37, 1, 1, 1, 1, 4, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
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, 57, 141, 141, 141, 141, 141, 141, 191, 191, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 141, 141, 141, 141, 191, 201, 201, 201, 201] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078894 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(F)=N2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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
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, 123, 41, 14, 14, 14, 8, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 123, 123, 14, 14, 14, 14, 8, 2, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 549
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078894 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078894
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078894/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078894/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078894
Building REAL300000078895
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078895'
/scratch/stefan/7769659/working/building/REAL300000078895 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078895

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078895/0 /scratch/stefan/7769659/working/building/REAL300000078895 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/953
`/scratch/stefan/7769659/working/3D/953' -> `0.mol2'
Preparing input files

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

`REAL300000078895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078895 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 3, 1, 1, 1] 7
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24])
total number of confs: 12
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078895 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 7, 7, 7, 7, 7, 7, 1, 1, 1, 4, 6, 7, 7, 7] 7
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078895 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078895
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078895/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078895
Building REAL300000078896
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078896'
/scratch/stefan/7769659/working/building/REAL300000078896 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078896

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078896/0 /scratch/stefan/7769659/working/building/REAL300000078896 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/954
`/scratch/stefan/7769659/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC(F)=N1)

`REAL300000078896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078896 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 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: [29, 27, 27, 27, 27, 27, 29, 27, 27, 27, 27, 27, 27, 29, 29, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 27, 29, 29, 29, 27, 27, 16, 4, 1, 1, 1] 31
rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 56
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078896 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 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: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 23, 27, 27, 27, 27, 27, 27, 3, 3, 3, 1, 3, 4, 3, 1, 1, 7, 23, 27, 27, 27] 31
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078896 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078896/1 /scratch/stefan/7769659/working/building/REAL300000078896 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/955
`/scratch/stefan/7769659/working/3D/955' -> `1.mol2'
Preparing input files

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

`REAL300000078896.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078896/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078896 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [154, 104, 104, 104, 104, 104, 138, 104, 104, 104, 104, 104, 104, 150, 150, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 104, 138, 138, 138, 104, 104, 46, 47, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 582
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078896 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2CN=NC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.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, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 46, 46, 104, 104, 103, 104, 104, 104, 3, 3, 3, 1, 3, 3, 3, 1, 1, 6, 6, 104, 104, 103] 201
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 34, 15, 16, 33, 29] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 172
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078896 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078896
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078896/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078896/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078896
Building REAL300000078897
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078897'
/scratch/stefan/7769659/working/building/REAL300000078897 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078897

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078897/0 /scratch/stefan/7769659/working/building/REAL300000078897 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/956
`/scratch/stefan/7769659/working/3D/956' -> `0.mol2'
Preparing input files

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

`REAL300000078897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078897 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 12, 12, 12, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 6, 2, 1, 1, 1] 12
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27])
total number of confs: 21
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078897 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CC=CC(F)=N1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 6, 12, 12, 12, 12] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078897 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078897
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078897/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078897
Building REAL300000078898
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078898'
/scratch/stefan/7769659/working/building/REAL300000078898 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078898

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078898/0 /scratch/stefan/7769659/working/building/REAL300000078898 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/957
`/scratch/stefan/7769659/working/3D/957' -> `0.mol2'
Preparing input files

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

`REAL300000078898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078898 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [186, 186, 186, 135, 64, 35, 64, 64, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 186, 186, 64, 64, 20, 4, 1, 1, 1, 64] 186
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 577
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078898 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [68, 42, 68, 9, 1, 1, 1, 1, 1, 1, 8, 8, 38, 64, 64, 64, 64, 64, 64, 1, 1, 1, 42, 42, 1, 1, 8, 38, 64, 64, 64, 1] 186
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 352
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078898 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078898/1 /scratch/stefan/7769659/working/building/REAL300000078898 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/958
`/scratch/stefan/7769659/working/3D/958' -> `1.mol2'
Preparing input files

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

`REAL300000078898.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078898/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078898 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 182, 79, 79, 79, 79, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 201, 201, 79, 79, 18, 19, 1, 1, 1, 79] 201
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 398
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078898 none O=C([O-])COC1=CC=C(CN=NC2=CC=CC(F)=N2)C=C1Cl NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 22, 30, 7, 1, 1, 1, 1, 1, 1, 7, 47, 47, 79, 79, 79, 79, 79, 79, 1, 1, 1, 22, 22, 1, 1, 7, 7, 79, 79, 79, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078898 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078898
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078898/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078898/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078898
Building REAL300000078899
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078899'
/scratch/stefan/7769659/working/building/REAL300000078899 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078899

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078899/0 /scratch/stefan/7769659/working/building/REAL300000078899 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/959
`/scratch/stefan/7769659/working/3D/959' -> `0.mol2'
Preparing input files

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

`REAL300000078899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078899 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 11, 7, 11, 11, 7, 11, 11, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 21, 11, 11, 4, 2, 1, 1, 1, 11, 11] 25
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078899 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(F)=N2)C=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [7, 7, 7, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 1, 1, 7, 7, 5, 1, 1, 7, 11, 11, 11, 11, 1, 1] 25
rigid atoms, others: [34, 35, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078899 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078899
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078899/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078899
Building REAL300000078900
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078900'
/scratch/stefan/7769659/working/building/REAL300000078900 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078900

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078900/0 /scratch/stefan/7769659/working/building/REAL300000078900 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/960
`/scratch/stefan/7769659/working/3D/960' -> `0.mol2'
Preparing input files

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

`REAL300000078900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078900 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(F)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 12, 4, 1, 1, 1, 16, 16] 16
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078900 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(F)=N3)C(F)=CC=C2S1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 9, 9, 15, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 9, 15, 16, 16, 16, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078900 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078900
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078900/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078900
Building REAL300000078901
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078901'
/scratch/stefan/7769659/working/building/REAL300000078901 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078901

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078901/0 /scratch/stefan/7769659/working/building/REAL300000078901 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/961
`/scratch/stefan/7769659/working/3D/961' -> `0.mol2'
Preparing input files

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

`REAL300000078901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 9, 9, 28, 40, 40, 40, 40, 40, 40, 1, 13, 13, 13, 1, 1, 9, 28, 40, 40, 40, 13, 13] 99
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 160
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 95, 99, 99, 99, 99, 99, 99, 13, 1, 1, 1, 13, 13, 50, 95, 99, 99, 99, 1, 1] 99
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 99, 99, 99, 99, 99, 40, 99, 40, 40, 40, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 40, 99, 99, 99, 40, 40, 17, 4, 1, 1, 1, 99, 99] 99
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 232
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078901 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078901/1 /scratch/stefan/7769659/working/building/REAL300000078901 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/962
`/scratch/stefan/7769659/working/3D/962' -> `1.mol2'
Preparing input files

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

`REAL300000078901.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078901/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 10, 18, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 9, 54, 54, 72, 72, 72, 72, 72, 72, 1, 10, 10, 10, 1, 1, 9, 9, 72, 72, 72, 10, 10] 201
rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 52, 181, 181, 201, 201, 201, 201, 201, 201, 10, 1, 1, 1, 10, 10, 52, 52, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078901 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC(F)=N3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 15, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 72, 201, 72, 72, 72, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 72, 72, 20, 21, 1, 1, 1, 201, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078901 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078901
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078901/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078901/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078901
Building REAL300000078902
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078902'
/scratch/stefan/7769659/working/building/REAL300000078902 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078902

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078902/0 /scratch/stefan/7769659/working/building/REAL300000078902 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/963
`/scratch/stefan/7769659/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1)

`REAL300000078902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078902 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 189, 159, 139, 47, 29, 29, 6, 29, 6, 11, 11, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 11, 201, 201, 201, 189, 189, 159, 159, 139, 139, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [48, 49, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51])
total number of confs: 810
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078902 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 76, 51, 41, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 21, 21, 11, 11, 1, 1, 100, 100, 100, 76, 76, 51, 51, 41, 41, 5, 5, 5, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 50, 51, 7, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 460
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078902 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078902
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078902/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078902
Building REAL300000078903
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078903'
/scratch/stefan/7769659/working/building/REAL300000078903 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078903

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078903/0 /scratch/stefan/7769659/working/building/REAL300000078903 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/964
`/scratch/stefan/7769659/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C(C)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1)

`REAL300000078903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078903 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 19, 15, 11, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 45, 45, 53, 61, 61, 1, 1, 25, 25, 25, 19, 19, 15, 15, 11, 11, 3, 3, 3, 1, 1, 23, 23, 23, 45, 45, 45, 45, 53, 53, 1, 1] 201
rigid atoms, others: [38, 7, 9, 10, 11, 12, 13, 49, 50, 24, 25, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078903 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078903
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078903/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078903
Building REAL300000078904
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078904'
/scratch/stefan/7769659/working/building/REAL300000078904 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078904

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078904/0 /scratch/stefan/7769659/working/building/REAL300000078904 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/965
`/scratch/stefan/7769659/working/3D/965' -> `0.mol2'
Preparing input files

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

`REAL300000078904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078904 none COCCCON=C(C)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 161, 114, 41, 25, 25, 2, 24, 2, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 161, 161, 114, 114, 23, 25, 25, 9, 9, 1, 1, 9, 9] 201
rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 894
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078904 none COCCCON=C(C)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [136, 115, 82, 54, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 136, 136, 136, 115, 115, 82, 82, 54, 54, 6, 6, 6, 1, 1, 9, 9, 1, 1] 201
rigid atoms, others: [35, 36, 7, 40, 9, 10, 11, 12, 13, 21, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 557
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078904 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078904
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078904/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078904
Building REAL300000078905
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078905'
/scratch/stefan/7769659/working/building/REAL300000078905 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078905

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078905/0 /scratch/stefan/7769659/working/building/REAL300000078905 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/966
`/scratch/stefan/7769659/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1)

`REAL300000078905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078905 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 153, 112, 33, 14, 14, 4, 14, 4, 4, 4, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 201, 201, 201, 201, 201, 153, 153, 112, 112, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 201
rigid atoms, others: [48, 49, 41, 42, 43, 44, 13, 46, 45, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51])
total number of confs: 847
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078905 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [163, 150, 109, 70, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 163, 163, 163, 150, 150, 109, 109, 70, 70, 6, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 50, 51, 7, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 696
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078905 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078905
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078905/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078905
Building REAL300000078906
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078906'
/scratch/stefan/7769659/working/building/REAL300000078906 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078906

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078906/0 /scratch/stefan/7769659/working/building/REAL300000078906 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/967
`/scratch/stefan/7769659/working/3D/967' -> `0.mol2'
Preparing input files

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

`REAL300000078906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078906 none COCCCON=C(C)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [112, 96, 82, 46, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 7, 20, 26, 26, 1, 1, 112, 112, 112, 96, 96, 82, 82, 46, 46, 5, 5, 5, 1, 1, 7, 20, 20, 1, 1] 201
rigid atoms, others: [35, 36, 7, 40, 9, 10, 11, 12, 13, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 542
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078906 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078906
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078906/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078906
Building REAL300000078907
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078907'
/scratch/stefan/7769659/working/building/REAL300000078907 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078907

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078907/0 /scratch/stefan/7769659/working/building/REAL300000078907 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/968
`/scratch/stefan/7769659/working/3D/968' -> `0.mol2'
Preparing input files

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

`REAL300000078907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078907 none COCCCON=C(C)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 67, 57, 31, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 28, 26, 1, 1, 70, 70, 70, 67, 67, 57, 57, 31, 31, 5, 5, 5, 1, 1, 5, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [43, 36, 37, 7, 9, 10, 11, 12, 13, 44, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 415
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078907 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078907
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078907/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078907
Building REAL300000078908
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078908'
/scratch/stefan/7769659/working/building/REAL300000078908 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078908

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078908/0 /scratch/stefan/7769659/working/building/REAL300000078908 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/969
`/scratch/stefan/7769659/working/3D/969' -> `0.mol2'
Preparing input files

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

`REAL300000078908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078908 none COCCCON=C(C)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 57, 47, 27, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 19, 31, 33, 39, 39, 1, 1, 61, 61, 61, 57, 57, 47, 47, 27, 27, 5, 5, 5, 1, 1, 5, 19, 19, 31, 31, 33, 33, 1, 1] 201
rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 46, 47, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078908 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078908
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078908/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078908
Building REAL300000078909
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078909'
/scratch/stefan/7769659/working/building/REAL300000078909 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078909

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078909/0 /scratch/stefan/7769659/working/building/REAL300000078909 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/970
`/scratch/stefan/7769659/working/3D/970' -> `0.mol2'
Preparing input files

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

`REAL300000078909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078909 none COCCCON=C(C)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [145, 126, 85, 53, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 13, 13, 1, 1, 145, 145, 145, 126, 126, 85, 85, 53, 53, 6, 6, 6, 1, 1, 5, 10, 10, 10, 1, 1] 201
rigid atoms, others: [43, 37, 38, 7, 9, 10, 11, 12, 13, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 667
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078909 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078909
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078909/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078909
Building REAL300000078910
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078910'
/scratch/stefan/7769659/working/building/REAL300000078910 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078910

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078910/0 /scratch/stefan/7769659/working/building/REAL300000078910 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/971
`/scratch/stefan/7769659/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078910 none COCCCON=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 70, 44, 28, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 41, 41, 89, 89, 89, 70, 70, 44, 44, 28, 28, 4, 1, 1, 1, 29, 29] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078910 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078910
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078910/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078910
Building REAL300000078911
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078911'
/scratch/stefan/7769659/working/building/REAL300000078911 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078911

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078911/0 /scratch/stefan/7769659/working/building/REAL300000078911 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/972
`/scratch/stefan/7769659/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1)

`REAL300000078911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078911 none COCCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 98, 33, 23, 23, 15, 15, 14, 15, 15, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 201, 201, 201, 201, 201, 150, 150, 98, 98, 23, 14, 15, 15, 5, 5, 1, 1, 1, 1, 15] 201
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 885
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078911 none COCCCON=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 70, 49, 27, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 15, 15, 15, 15, 15, 15, 17, 17, 1, 78, 78, 78, 70, 70, 49, 49, 27, 27, 3, 1, 1, 1, 7, 7, 15, 15, 15, 15, 1] 201
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 381
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078911 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078911
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078911/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078911
Building REAL300000078912
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078912'
/scratch/stefan/7769659/working/building/REAL300000078912 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078912

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078912/0 /scratch/stefan/7769659/working/building/REAL300000078912 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/973
`/scratch/stefan/7769659/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1)

`REAL300000078912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078912 none COCCCON=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [97, 93, 67, 41, 9, 4, 4, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 97, 97, 97, 93, 93, 66, 66, 41, 41, 4, 1, 1, 5, 5, 1] 136
rigid atoms, others: [32, 33, 36, 7, 8, 9, 10, 11, 12, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078912 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078912
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078912/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078912
Building REAL300000078913
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078913'
/scratch/stefan/7769659/working/building/REAL300000078913 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078913

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078913/0 /scratch/stefan/7769659/working/building/REAL300000078913 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/974
`/scratch/stefan/7769659/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1)

`REAL300000078913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078913 none COCCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 134, 77, 21, 13, 13, 13, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 201, 201, 201, 201, 201, 134, 134, 77, 77, 13, 13, 13, 8, 8, 1, 2, 2, 2, 13, 13] 201
rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 952
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078913 none COCCCON=CC1=CC=C(OCC2=CC(C)=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 28, 14, 4, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 13, 13, 13, 13, 13, 23, 23, 13, 1, 1, 44, 44, 44, 40, 40, 28, 28, 14, 14, 2, 1, 1, 2, 2, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 44, 43, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078913 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078913
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078913/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078913
Building REAL300000078914
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078914'
/scratch/stefan/7769659/working/building/REAL300000078914 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078914

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078914/0 /scratch/stefan/7769659/working/building/REAL300000078914 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/975
`/scratch/stefan/7769659/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000078914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078914 none COCCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 99, 35, 23, 23, 13, 13, 12, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 201, 201, 201, 201, 201, 157, 157, 99, 99, 23, 12, 13, 13, 7, 7, 1, 1, 1, 1, 13] 201
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 885
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078914 none COCCCON=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 28, 20, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 41, 41, 41, 38, 38, 28, 28, 20, 20, 2, 1, 1, 1, 3, 3, 13, 13, 13, 13, 1] 201
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078914 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078914
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078914/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078914
Building REAL300000078915
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078915'
/scratch/stefan/7769659/working/building/REAL300000078915 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078915

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078915/0 /scratch/stefan/7769659/working/building/REAL300000078915 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/976
`/scratch/stefan/7769659/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1)

`REAL300000078915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078915 none COCCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 139, 99, 28, 16, 16, 15, 15, 15, 15, 10, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 15, 15, 201, 201, 201, 201, 201, 139, 139, 99, 99, 16, 15, 15, 6, 6, 1, 1, 15, 15] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 881
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078915 none COCCCON=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 29, 17, 5, 3, 3, 1, 1, 1, 1, 1, 1, 2, 6, 15, 15, 16, 16, 15, 15, 15, 1, 1, 51, 51, 51, 45, 45, 29, 29, 17, 17, 3, 1, 1, 6, 6, 15, 15, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 249
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078915 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078915
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078915/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078915
Building REAL300000078916
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078916'
/scratch/stefan/7769659/working/building/REAL300000078916 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078916

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078916/0 /scratch/stefan/7769659/working/building/REAL300000078916 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/977
`/scratch/stefan/7769659/working/3D/977' -> `0.mol2'
Preparing input files

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

`REAL300000078916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078916 none COCCCON=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 24, 16, 6, 3, 3, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 40, 40, 1, 1, 37, 37, 37, 33, 33, 23, 23, 16, 16, 3, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078916 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078916
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078916/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078916
Building REAL300000078917
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078917'
/scratch/stefan/7769659/working/building/REAL300000078917 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078917

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078917/0 /scratch/stefan/7769659/working/building/REAL300000078917 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/978
`/scratch/stefan/7769659/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C(Br)C=C(C(=O)[O-])N1C)

`REAL300000078917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078917 none COCCCON=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 153, 96, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 153, 153, 96, 96, 9, 1, 2, 2, 2] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31])
total number of confs: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078917 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078917
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078917/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078917
Building REAL300000078918
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078918'
/scratch/stefan/7769659/working/building/REAL300000078918 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078918

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078918/0 /scratch/stefan/7769659/working/building/REAL300000078918 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/979
`/scratch/stefan/7769659/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCC(=O)[O-])C(Br)=C1)

`REAL300000078918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078918 none COCCCON=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 79, 56, 33, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 23, 30, 30, 1, 1, 1, 83, 83, 83, 79, 79, 55, 55, 34, 34, 5, 1, 1, 23, 23, 1] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 463
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078918 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078918
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078918/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078918
Building REAL300000078919
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078919'
/scratch/stefan/7769659/working/building/REAL300000078919 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078919

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078919/0 /scratch/stefan/7769659/working/building/REAL300000078919 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/980
`/scratch/stefan/7769659/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C2C=C(C(=O)[O-])OC2=C(OC)C=C1)

`REAL300000078919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078919 none COCCCON=CC1=C2C=C(C(=O)[O-])OC2=C(OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 111, 68, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 201, 201, 201, 173, 173, 111, 111, 68, 68, 4, 1, 4, 4, 4, 1, 1] 201
rigid atoms, others: [32, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 33, 35, 34, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 867
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078919 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078919
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078919/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078919
Building REAL300000078920
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078920'
/scratch/stefan/7769659/working/building/REAL300000078920 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078920

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078920/0 /scratch/stefan/7769659/working/building/REAL300000078920 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/981
`/scratch/stefan/7769659/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1)

`REAL300000078920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078920 none COCCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 190, 120, 63, 58, 58, 26, 24, 36, 36, 21, 10, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 36, 36, 201, 201, 201, 201, 201, 190, 190, 120, 120, 58, 36, 36, 10, 10, 6, 6, 1, 36] 201
rigid atoms, others: [42, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43])
total number of confs: 943
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078920 none COCCCON=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', '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, 5, 5, 12, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 32, 27, 13, 4, 2, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 35, 35, 35, 32, 32, 27, 27, 13, 13, 2, 1, 1, 12, 12, 12, 12, 36, 1] 201
rigid atoms, others: [43, 36, 37, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078920 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078920
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078920/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078920
Building REAL300000078921
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078921'
/scratch/stefan/7769659/working/building/REAL300000078921 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078921

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078921/0 /scratch/stefan/7769659/working/building/REAL300000078921 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/982
`/scratch/stefan/7769659/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(OC)=C(OCC(=O)[O-])C=C1[N+](=O)[O-])

`REAL300000078921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078921 none COCCCON=CC1=CC(OC)=C(OCC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 72, 51, 31, 7, 3, 3, 1, 1, 1, 1, 1, 3, 1, 1, 9, 14, 18, 18, 1, 1, 1, 2, 2, 80, 80, 80, 72, 72, 51, 51, 31, 31, 3, 1, 3, 3, 3, 14, 14, 1] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 13, 14, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 12, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39])
total number of confs: 403
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078921 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078921
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078921/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078921
Building REAL300000078922
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078922'
/scratch/stefan/7769659/working/building/REAL300000078922 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078922

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078922/0 /scratch/stefan/7769659/working/building/REAL300000078922 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/983
`/scratch/stefan/7769659/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-])

`REAL300000078922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078922 none COCCCON=CC1=CC(C(F)(F)F)=CC=C1N(C)CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 75, 48, 26, 6, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 15, 23, 23, 98, 98, 98, 75, 75, 48, 48, 26, 26, 2, 1, 1, 1, 4, 4, 4, 15, 15] 201
rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41])
total number of confs: 484
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078922 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078922
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078922/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078922
Building REAL300000078923
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078923'
/scratch/stefan/7769659/working/building/REAL300000078923 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078923

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078923/0 /scratch/stefan/7769659/working/building/REAL300000078923 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/984
`/scratch/stefan/7769659/working/3D/984' -> `0.mol2'
Preparing input files

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

`REAL300000078923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078923 none COCCCON=C(C)C1=CC=C(OC2=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', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 117, 41, 28, 28, 9, 28, 4, 9, 9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 201, 201, 201, 201, 201, 157, 157, 117, 117, 28, 28, 28, 9, 9, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 884
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078923 none COCCCON=C(C)C1=CC=C(OC2=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', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 103, 71, 46, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 107, 107, 107, 103, 103, 71, 71, 46, 46, 5, 5, 5, 1, 1, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [43, 37, 38, 7, 9, 10, 11, 12, 13, 44, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42])
total number of confs: 473
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078923 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078923
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078923/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078923
Building REAL300000078924
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078924'
/scratch/stefan/7769659/working/building/REAL300000078924 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078924

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078924/0 /scratch/stefan/7769659/working/building/REAL300000078924 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/985
`/scratch/stefan/7769659/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCCC(=O)[O-])C(OC)=C1)

`REAL300000078924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078924 none COCCCON=CC1=CC=C(OCCC(=O)[O-])C(OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 40, 25, 7, 3, 3, 1, 1, 1, 1, 1, 1, 9, 14, 14, 24, 22, 1, 1, 3, 1, 62, 62, 62, 57, 57, 40, 40, 25, 25, 3, 1, 1, 14, 14, 14, 14, 3, 3, 3, 1] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 18, 19, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078924 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078924
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078924/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078924
Building REAL300000078925
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078925'
/scratch/stefan/7769659/working/building/REAL300000078925 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078925

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078925/0 /scratch/stefan/7769659/working/building/REAL300000078925 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/986
`/scratch/stefan/7769659/working/3D/986' -> `0.mol2'
Preparing input files

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

`REAL300000078925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078925 none COCCCON=C(C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 32, 19, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 19, 26, 37, 45, 45, 1, 34, 34, 34, 34, 34, 32, 32, 19, 19, 5, 5, 5, 1, 1, 1, 19, 19, 26, 26, 37, 37, 1] 201
rigid atoms, others: [34, 35, 36, 7, 9, 10, 11, 12, 13, 14, 43, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 335
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078925 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078925
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078925/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078925
Building REAL300000078926
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078926'
/scratch/stefan/7769659/working/building/REAL300000078926 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078926

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078926/0 /scratch/stefan/7769659/working/building/REAL300000078926 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/987
`/scratch/stefan/7769659/working/3D/987' -> `0.mol2'
Preparing input files

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

`REAL300000078926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078926 none COCCCON=C(C)CCC1=CC=C(OC(C)C(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 85, 65, 44, 14, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 20, 20, 1, 1, 90, 90, 90, 85, 85, 65, 65, 44, 44, 12, 12, 12, 3, 3, 1, 1, 1, 1, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 463
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078926 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078926
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078926/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078926
Building REAL300000078927
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078927'
/scratch/stefan/7769659/working/building/REAL300000078927 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078927

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078927/0 /scratch/stefan/7769659/working/building/REAL300000078927 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/988
`/scratch/stefan/7769659/working/3D/988' -> `0.mol2'
Preparing input files

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

`REAL300000078927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078927 none COCCCON=C(C)CCC1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 96, 78, 51, 16, 12, 12, 4, 12, 2, 1, 1, 1, 1, 1, 1, 6, 14, 27, 27, 1, 1, 100, 100, 100, 96, 96, 78, 78, 51, 51, 12, 12, 12, 4, 4, 2, 2, 1, 1, 14, 14, 1, 1] 201
rigid atoms, others: [43, 38, 39, 10, 11, 12, 13, 14, 15, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 524
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078927 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078927
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078927/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078927
Building REAL300000078928
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078928'
/scratch/stefan/7769659/working/building/REAL300000078928 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078928

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078928/0 /scratch/stefan/7769659/working/building/REAL300000078928 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/989
`/scratch/stefan/7769659/working/3D/989' -> `0.mol2'
Preparing input files

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

`REAL300000078928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078928 none COCCCON=C(C)CCC1=CC=C(OCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 48, 32, 16, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 1, 1, 66, 66, 66, 62, 62, 48, 48, 32, 32, 12, 12, 12, 3, 3, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078928 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078928
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078928/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078928
Building REAL300000078929
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078929'
/scratch/stefan/7769659/working/building/REAL300000078929 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078929

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078929/0 /scratch/stefan/7769659/working/building/REAL300000078929 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/990
`/scratch/stefan/7769659/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000078929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078929 none COCCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 163, 109, 61, 57, 57, 24, 57, 10, 5, 5, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 10, 201, 201, 201, 201, 201, 163, 163, 109, 109, 57, 57, 57, 24, 24, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53])
total number of confs: 985
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078929 none COCCCON=C(C)CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 59, 43, 32, 16, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 11, 11, 10, 1, 1, 63, 63, 63, 59, 59, 43, 43, 32, 32, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [45, 43, 15, 9, 10, 11, 12, 13, 14, 44, 52, 53, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51])
total number of confs: 287
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078929 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078929
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078929/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078929
Building REAL300000078930
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078930'
/scratch/stefan/7769659/working/building/REAL300000078930 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078930

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078930/0 /scratch/stefan/7769659/working/building/REAL300000078930 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/991
`/scratch/stefan/7769659/working/3D/991' -> `0.mol2'
Preparing input files

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

`REAL300000078930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078930 none CCC(=NOCCCOC)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 12, 5, 5, 5, 12, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 1, 6, 6, 9, 26, 45, 51, 52, 1, 1, 1, 1, 1, 6, 7, 16, 16, 16, 21, 22, 1, 1, 11, 11, 11, 11, 11, 26, 26, 45, 45, 51, 51, 52, 52, 52, 1, 1, 8, 8, 15, 15, 16, 16, 16, 15, 1, 1] 201
rigid atoms, others: [2, 38, 39, 10, 11, 12, 13, 14, 48, 49, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 324
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078930 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078930
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078930/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078930
Building REAL300000078931
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078931'
/scratch/stefan/7769659/working/building/REAL300000078931 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078931

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078931/0 /scratch/stefan/7769659/working/building/REAL300000078931 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/992
`/scratch/stefan/7769659/working/3D/992' -> `0.mol2'
Preparing input files

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

`REAL300000078931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078931 none COCCCON=C(C)C1=CC=C(OCCCC(=O)[O-])C(OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 65, 58, 42, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 11, 11, 18, 23, 23, 1, 1, 3, 1, 67, 67, 67, 65, 65, 58, 58, 42, 42, 9, 9, 9, 1, 1, 11, 11, 11, 11, 18, 18, 3, 3, 3, 1] 201
rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 47, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078931 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078931
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078931/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078931
Building REAL300000078932
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078932'
/scratch/stefan/7769659/working/building/REAL300000078932 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078932

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078932/0 /scratch/stefan/7769659/working/building/REAL300000078932 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/993
`/scratch/stefan/7769659/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1)

`REAL300000078932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078932 none COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 144, 96, 21, 5, 5, 5, 5, 1, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 186, 186, 144, 144, 96, 96, 5, 5, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [32, 33, 34, 35, 9, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 875
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078932 none COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 86, 58, 32, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 5, 1, 107, 107, 107, 86, 86, 58, 58, 32, 32, 1, 1, 5, 5, 4, 5, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 13, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078932 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078932
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078932/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078932
Building REAL300000078933
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078933'
/scratch/stefan/7769659/working/building/REAL300000078933 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078933

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078933/0 /scratch/stefan/7769659/working/building/REAL300000078933 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/994
`/scratch/stefan/7769659/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1)

`REAL300000078933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078933 none COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 185, 144, 96, 21, 5, 5, 5, 5, 1, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 185, 185, 144, 144, 96, 96, 5, 5, 1, 1, 1, 1, 5, 5] 201
rigid atoms, others: [32, 33, 34, 35, 9, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 871
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078933 none COCCCON=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 87, 58, 32, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 2, 5, 5, 5, 1, 110, 110, 110, 87, 87, 58, 58, 32, 32, 1, 1, 5, 5, 3, 5, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 13, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 477
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078933 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078933
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078933/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078933
Building REAL300000078934
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078934'
/scratch/stefan/7769659/working/building/REAL300000078934 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078934

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078934/0 /scratch/stefan/7769659/working/building/REAL300000078934 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/995
`/scratch/stefan/7769659/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-])

`REAL300000078934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078934 none COCCCON=C(C)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 73, 50, 32, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 46, 46, 87, 87, 87, 73, 73, 50, 50, 32, 32, 3, 3, 3, 1, 1, 1, 29, 29] 201
rigid atoms, others: [33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37])
total number of confs: 523
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078934 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078934
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078934/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078934
Building REAL300000078935
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078935'
/scratch/stefan/7769659/working/building/REAL300000078935 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078935

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078935/0 /scratch/stefan/7769659/working/building/REAL300000078935 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/996
`/scratch/stefan/7769659/working/3D/996' -> `0.mol2'
Preparing input files

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

`REAL300000078935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078935 none COCCCON=C(C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', '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, 8, 1, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 163, 111, 27, 9, 9, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 195, 195, 163, 163, 111, 111, 9, 9, 9, 2, 2, 1, 1, 2, 2, 2, 1] 201
rigid atoms, others: [37, 38, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41])
total number of confs: 888
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078935 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078935
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078935/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078935
Building REAL300000078936
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078936'
/scratch/stefan/7769659/working/building/REAL300000078936 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078936

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078936/0 /scratch/stefan/7769659/working/building/REAL300000078936 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/997
`/scratch/stefan/7769659/working/3D/997' -> `0.mol2'
Preparing input files

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

`REAL300000078936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078936 none COCCCON=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 146, 88, 36, 28, 28, 26, 26, 26, 26, 26, 7, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 197, 197, 146, 146, 88, 88, 28, 26, 26, 26, 3, 1, 1, 1, 1, 1, 26] 201
rigid atoms, others: [39, 40, 41, 42, 43, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44])
total number of confs: 855
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078936 none COCCCON=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 45, 24, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 21, 23, 23, 21, 26, 26, 21, 26, 26, 1, 72, 72, 72, 62, 62, 45, 45, 24, 24, 2, 1, 1, 1, 21, 26, 26, 21, 26, 26, 1] 201
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
total number of confs: 393
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078936 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078936
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078936/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078936
Building REAL300000078937
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078937'
/scratch/stefan/7769659/working/building/REAL300000078937 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078937

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078937/0 /scratch/stefan/7769659/working/building/REAL300000078937 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/998
`/scratch/stefan/7769659/working/3D/998' -> `0.mol2'
Preparing input files

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

`REAL300000078937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078937 none COCCCON=C(C)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [195, 160, 96, 49, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 195, 195, 195, 160, 160, 96, 96, 49, 49, 3, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 201
rigid atoms, others: [34, 35, 36, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 875
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078937 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078937
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078937/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078937
Building REAL300000078938
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078938'
/scratch/stefan/7769659/working/building/REAL300000078938 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078938

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078938/0 /scratch/stefan/7769659/working/building/REAL300000078938 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/999
`/scratch/stefan/7769659/working/3D/999' -> `0.mol2'
Preparing input files

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

`REAL300000078938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078938 none COCCCON=CC1=CC=C(C2=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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 159, 113, 37, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 201, 201, 201, 201, 201, 159, 159, 113, 113, 6, 3, 3, 1, 1, 1, 1, 3, 3] 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])
total number of confs: 836
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078938 none COCCCON=CC1=CC=C(C2=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', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [148, 136, 106, 69, 21, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 148, 148, 148, 136, 136, 105, 105, 70, 70, 5, 1, 1, 3, 3, 3, 3, 1, 1] 201
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 40, 21, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 625
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078938 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078938
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078938/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078938
Building REAL300000078939
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078939'
/scratch/stefan/7769659/working/building/REAL300000078939 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078939

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078939/0 /scratch/stefan/7769659/working/building/REAL300000078939 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1000
`/scratch/stefan/7769659/working/3D/1000' -> `0.mol2'
Preparing input files

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

`REAL300000078939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078939 none COCCCON=CC1=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', '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, 8, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 79, 53, 33, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 13, 13, 1, 1, 3, 1, 90, 90, 90, 79, 79, 52, 52, 34, 34, 5, 1, 9, 10, 10, 10, 4, 4, 4, 1] 201
rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078939 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078939
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078939/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078939
Building REAL300000078940
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078940'
/scratch/stefan/7769659/working/building/REAL300000078940 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078940

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078940/0 /scratch/stefan/7769659/working/building/REAL300000078940 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1001
`/scratch/stefan/7769659/working/3D/1001' -> `0.mol2'
Preparing input files

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

`REAL300000078940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078940 none COCCCON=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 123, 45, 22, 22, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 201, 201, 201, 201, 201, 157, 157, 123, 123, 22, 13, 13, 1, 1, 2, 1] 402
rigid atoms, others: [35, 36, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37])
total number of confs: 804
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078940 none COCCCON=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 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: [144, 127, 86, 45, 12, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 12, 12, 13, 13, 13, 13, 13, 1, 144, 144, 144, 127, 127, 85, 85, 45, 45, 4, 1, 1, 13, 13, 26, 13] 402
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 665
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078940 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078940
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078940/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078940
Building REAL300000078941
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078941'
/scratch/stefan/7769659/working/building/REAL300000078941 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078941

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078941/0 /scratch/stefan/7769659/working/building/REAL300000078941 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1002
`/scratch/stefan/7769659/working/3D/1002' -> `0.mol2'
Preparing input files

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

`REAL300000078941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078941 none COCCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 167, 127, 48, 23, 23, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 167, 167, 127, 127, 23, 6, 6, 1, 1, 1, 1] 201
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])
total number of confs: 840
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078941 none COCCCON=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 135, 98, 62, 13, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 1, 155, 155, 155, 135, 135, 98, 98, 62, 62, 5, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078941 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078941
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078941/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078941
Building REAL300000078942
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078942'
/scratch/stefan/7769659/working/building/REAL300000078942 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078942

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078942/0 /scratch/stefan/7769659/working/building/REAL300000078942 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1003
`/scratch/stefan/7769659/working/3D/1003' -> `0.mol2'
Preparing input files

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

`REAL300000078942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078942 none COCCCON=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 108, 40, 21, 21, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 201, 201, 201, 201, 201, 149, 149, 108, 108, 21, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 856
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078942 none COCCCON=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 93, 64, 36, 12, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 111, 111, 111, 93, 93, 64, 64, 36, 36, 4, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078942 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078942
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078942/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078942
Building REAL300000078943
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078943'
/scratch/stefan/7769659/working/building/REAL300000078943 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078943

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078943/0 /scratch/stefan/7769659/working/building/REAL300000078943 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1004
`/scratch/stefan/7769659/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(C(=O)[O-])=CC=C1Br)

`REAL300000078943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078943 none COCCCON=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', '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, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 104, 32, 10, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 104, 104, 10, 1, 1, 1] 201
rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 875
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078943 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078943
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078943/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078943
Building REAL300000078944
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078944'
/scratch/stefan/7769659/working/building/REAL300000078944 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078944

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078944/0 /scratch/stefan/7769659/working/building/REAL300000078944 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1005
`/scratch/stefan/7769659/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1O)

`REAL300000078944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078944 none COCCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 167, 104, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 167, 167, 104, 104, 11, 1, 1, 2] 402
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 876
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078944 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078944/1 /scratch/stefan/7769659/working/building/REAL300000078944 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1006
`/scratch/stefan/7769659/working/3D/1006' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-])

`REAL300000078944.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078944/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078944 none COCCCON=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 169, 136, 86, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 169, 169, 136, 136, 86, 86, 6, 1, 1] 174
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 750
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078944 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078944
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078944/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078944/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078944
Building REAL300000078945
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078945'
/scratch/stefan/7769659/working/building/REAL300000078945 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078945

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078945/0 /scratch/stefan/7769659/working/building/REAL300000078945 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1007
`/scratch/stefan/7769659/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-])

`REAL300000078945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078945 none COCCCON=CC1=CC(Br)=CC(OC)=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 74, 45, 26, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 2, 8, 16, 16, 106, 106, 106, 74, 74, 45, 45, 26, 26, 4, 1, 1, 4, 4, 4, 8, 8] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 463
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078945 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078945
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078945/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078945
Building REAL300000078946
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078946'
/scratch/stefan/7769659/working/building/REAL300000078946 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078946

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078946/0 /scratch/stefan/7769659/working/building/REAL300000078946 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1008
`/scratch/stefan/7769659/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1)

`REAL300000078946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078946 none COCCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 144, 99, 30, 18, 18, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 144, 144, 99, 99, 18, 16, 16, 9, 9, 1, 1, 16, 16] 201
rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 912
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078946 none COCCCON=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 75, 43, 22, 6, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 1, 1, 95, 95, 95, 75, 75, 43, 43, 22, 22, 4, 1, 1, 2, 2, 16, 16, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 408
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078946 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078946
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078946/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078946
Building REAL300000078947
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078947'
/scratch/stefan/7769659/working/building/REAL300000078947 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078947

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078947/0 /scratch/stefan/7769659/working/building/REAL300000078947 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1009
`/scratch/stefan/7769659/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC(I)=CC(C(=O)[O-])=C1)

`REAL300000078947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078947 none COCCCON=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 194, 148, 98, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 194, 194, 147, 147, 99, 99, 6, 1, 1, 1] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 871
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078947 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078947
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078947/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078947
Building REAL300000078948
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078948'
/scratch/stefan/7769659/working/building/REAL300000078948 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078948

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078948/0 /scratch/stefan/7769659/working/building/REAL300000078948 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1010
`/scratch/stefan/7769659/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21)

`REAL300000078948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078948 none COCCCON=CC1=C(O)C(C(=O)[O-])=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', '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', '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, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 155, 107, 29, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 155, 107, 107, 11, 2, 1, 1, 1, 1, 1] 402
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 865
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078948 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078948
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078948/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078948
Building REAL300000078949
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078949'
/scratch/stefan/7769659/working/building/REAL300000078949 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078949

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078949/0 /scratch/stefan/7769659/working/building/REAL300000078949 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1011
`/scratch/stefan/7769659/working/3D/1011' -> `0.mol2'
Preparing input files

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

`REAL300000078949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078949 none COCCCON=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 143, 104, 78, 21, 11, 11, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 5, 5, 155, 155, 155, 143, 143, 104, 104, 78, 78, 11, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201
rigid atoms, others: [36, 37, 38, 41, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43])
total number of confs: 655
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078949 none COCCCON=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 56, 42, 25, 5, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 5, 1, 1, 70, 70, 70, 56, 56, 41, 41, 25, 25, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078949 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078949
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078949/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078949
Building REAL300000078950
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078950'
/scratch/stefan/7769659/working/building/REAL300000078950 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078950

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078950/0 /scratch/stefan/7769659/working/building/REAL300000078950 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1012
`/scratch/stefan/7769659/working/3D/1012' -> `0.mol2'
Preparing input files

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

`REAL300000078950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078950 none CCOC1=CC(C=NOCCCOC)=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 12, 5, 5, 5, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 2, 2, 6, 22, 40, 48, 51, 1, 1, 1, 1, 7, 21, 35, 35, 3, 3, 3, 3, 3, 1, 2, 22, 22, 39, 39, 48, 48, 51, 51, 51, 1, 1, 21, 21] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 38, 14, 15, 16, 17, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078950 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078950
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078950/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078950
Building REAL300000078951
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078951'
/scratch/stefan/7769659/working/building/REAL300000078951 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078951

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078951/0 /scratch/stefan/7769659/working/building/REAL300000078951 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1013
`/scratch/stefan/7769659/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-])

`REAL300000078951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078951 none COCCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 160, 56, 29, 29, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 201, 201, 201, 201, 201, 191, 191, 160, 160, 29, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 798
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078951 none COCCCON=CC1=CN(C2CCOCC2)N=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [122, 115, 97, 53, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 3, 3, 122, 122, 122, 115, 115, 96, 96, 54, 54, 3, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [32, 7, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 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: 547
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078951 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078951
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078951/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078951
Building REAL300000078952
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078952'
/scratch/stefan/7769659/working/building/REAL300000078952 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078952

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078952/0 /scratch/stefan/7769659/working/building/REAL300000078952 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1014
`/scratch/stefan/7769659/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21)

`REAL300000078952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078952 none COCCCON=CC1=C(C(=O)[O-])N(C)C2=CC=C(F)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 86, 78, 57, 20, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 86, 86, 78, 78, 57, 57, 5, 2, 2, 2, 1, 1, 1] 88
rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 362
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078952 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078952
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078952/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078952
Building REAL300000078953
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078953'
/scratch/stefan/7769659/working/building/REAL300000078953 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078953

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078953/0 /scratch/stefan/7769659/working/building/REAL300000078953 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1015
`/scratch/stefan/7769659/working/3D/1015' -> `0.mol2'
Preparing input files

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

`REAL300000078953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078953 none COCCCON=C(C)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [142, 135, 108, 78, 24, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 135, 135, 108, 108, 78, 78, 6, 6, 6, 1, 1, 1, 1] 142
rigid atoms, others: [33, 34, 35, 36, 7, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 605
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078953 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078953
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078953/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078953
Building REAL300000078954
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078954'
/scratch/stefan/7769659/working/building/REAL300000078954 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078954

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078954/0 /scratch/stefan/7769659/working/building/REAL300000078954 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1016
`/scratch/stefan/7769659/working/3D/1016' -> `0.mol2'
Preparing input files

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

`REAL300000078954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078954 none COCCCON=CC1=C(C(=O)[O-])C=C(Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 11, 11, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [185, 178, 139, 83, 19, 3, 3, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 186, 186, 186, 178, 178, 139, 139, 83, 83, 3, 1] 201
rigid atoms, others: [7, 8, 9, 10, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 799
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078954 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078954
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078954/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078954
Building REAL300000078955
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078955'
/scratch/stefan/7769659/working/building/REAL300000078955 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078955

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078955/0 /scratch/stefan/7769659/working/building/REAL300000078955 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1017
`/scratch/stefan/7769659/working/3D/1017' -> `0.mol2'
Preparing input files

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

`REAL300000078955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078955 none COCCCON=C(C)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 8, 1, 5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 101, 84, 64, 15, 5, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 101, 101, 84, 84, 64, 64, 5, 5, 5, 1, 1, 1, 1, 1] 105
rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078955 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078955
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078955/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078955
Building REAL300000078956
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078956'
/scratch/stefan/7769659/working/building/REAL300000078956 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078956

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078956/0 /scratch/stefan/7769659/working/building/REAL300000078956 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1018
`/scratch/stefan/7769659/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1)

`REAL300000078956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078956 none COCCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 127, 73, 63, 63, 63, 63, 63, 63, 63, 63, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 174, 127, 127, 63, 63, 63, 63, 63, 8, 8, 1, 1] 201
rigid atoms, others: [40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078956 none COCCCON=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 24, 18, 12, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 63, 63, 63, 63, 63, 63, 63, 26, 26, 26, 24, 24, 18, 18, 12, 12, 2, 1, 1, 1, 1, 21, 21, 63, 63] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078956 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078956
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078956/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078956
Building REAL300000078957
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078957'
/scratch/stefan/7769659/working/building/REAL300000078957 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078957

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078957/0 /scratch/stefan/7769659/working/building/REAL300000078957 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1019
`/scratch/stefan/7769659/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=CC(Br)=C1C(=O)[O-])

`REAL300000078957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078957 none COCCCON=CC1=CC=CC(Br)=C1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 124, 111, 69, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 127, 127, 127, 124, 124, 111, 111, 70, 70, 6, 1, 1, 1] 127
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078957 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078957
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078957/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078957
Building REAL300000078958
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078958'
/scratch/stefan/7769659/working/building/REAL300000078958 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078958

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078958/0 /scratch/stefan/7769659/working/building/REAL300000078958 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1020
`/scratch/stefan/7769659/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C(C(=O)[O-])NC2=CC(OC)=CC(OC)=C21)

`REAL300000078958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078958 none COCCCON=CC1=C(C(=O)[O-])NC2=CC(OC)=CC(OC)=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [195, 173, 123, 83, 23, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 3, 1, 195, 195, 195, 173, 173, 123, 123, 83, 83, 7, 1, 1, 2, 2, 2, 1, 4, 4, 4] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 39, 13, 14, 15, 16, 17, 19, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 18, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42])
total number of confs: 838
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078958 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078958
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078958/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078958
Building REAL300000078959
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078959'
/scratch/stefan/7769659/working/building/REAL300000078959 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078959

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078959/0 /scratch/stefan/7769659/working/building/REAL300000078959 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1021
`/scratch/stefan/7769659/working/3D/1021' -> `0.mol2'
Preparing input files

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

`REAL300000078959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078959 none COCCCON=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 85, 62, 32, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 19, 27, 27, 1, 1, 1, 94, 94, 94, 85, 85, 61, 61, 33, 33, 5, 1, 1, 19, 19, 1] 201
rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 497
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078959 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078959
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078959/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078959
Building REAL300000078960
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078960'
/scratch/stefan/7769659/working/building/REAL300000078960 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078960

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078960/0 /scratch/stefan/7769659/working/building/REAL300000078960 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1022
`/scratch/stefan/7769659/working/3D/1022' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1)

`REAL300000078960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078960 none COCCCON=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 73, 54, 34, 8, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 33, 33, 1, 1, 98, 98, 98, 73, 73, 53, 53, 34, 34, 3, 1, 1, 9, 25, 25, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 7, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 497
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078960 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078960
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078960/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078960
Building REAL300000078961
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078961'
/scratch/stefan/7769659/working/building/REAL300000078961 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078961

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078961/0 /scratch/stefan/7769659/working/building/REAL300000078961 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1023
`/scratch/stefan/7769659/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCON=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F)

`REAL300000078961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078961 none COCCCON=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 105, 34, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 158, 158, 105, 105, 12, 1, 1, 1] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 877
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078961 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078961
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078961/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078961
Building REAL300000078962
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078962'
/scratch/stefan/7769659/working/building/REAL300000078962 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078962

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078962/0 /scratch/stefan/7769659/working/building/REAL300000078962 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1024
`/scratch/stefan/7769659/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=CC=C1OCC(=O)[O-])

`REAL300000078962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078962 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 33, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 58, 58, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 33, 33, 10, 4, 1, 1, 1, 1, 33, 33] 201
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 352
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078962 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 23, 48, 48, 66, 66, 48, 66, 66, 66, 139, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 23, 48, 66, 66, 66, 66, 201, 201] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 655
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078962 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078962
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078962/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078962
Building REAL300000078963
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078963'
/scratch/stefan/7769659/working/building/REAL300000078963 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078963

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078963/0 /scratch/stefan/7769659/working/building/REAL300000078963 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1025
`/scratch/stefan/7769659/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=O)[O-])C=C1)

`REAL300000078963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078963 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=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.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 35, 10, 4, 4, 1, 1, 1, 1, 1, 1, 6, 18, 31, 31, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 35, 35, 10, 4, 1, 1, 18, 18, 1, 1] 201
rigid atoms, others: [38, 39, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078963 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=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.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 45, 45, 57, 57, 45, 45, 133, 201, 201, 201, 57, 57, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 21, 45, 57, 57, 201, 201, 57, 57] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078963 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078963
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078963/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078963
Building REAL300000078964
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078964'
/scratch/stefan/7769659/working/building/REAL300000078964 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078964

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078964/0 /scratch/stefan/7769659/working/building/REAL300000078964 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1026
`/scratch/stefan/7769659/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC=C1N(C)C)CCC2)

`REAL300000078964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078964 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC=C1N(C)C)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 131, 131, 131, 131, 131, 131, 38, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 131, 131, 131, 131, 131, 131] 131
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 232
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078964 none CC1=C(C(=O)[O-])OC2=C1C(=NNCC1=CC=CC=C1N(C)C)CCC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 53, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 2, 2, 2, 8, 53, 53, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1] 131
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 44, 45, 46, 43, 41, 22, 23, 24, 42] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 302
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078964 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078964
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078964/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078964
Building REAL300000078965
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078965'
/scratch/stefan/7769659/working/building/REAL300000078965 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078965

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078965/0 /scratch/stefan/7769659/working/building/REAL300000078965 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1027
`/scratch/stefan/7769659/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=CC(C=NNCC2=CC=CC=C2N(C)C)=C1)C(=O)[O-])

`REAL300000078965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078965 none CC(OC1=CC=CC(C=NNCC2=CC=CC=C2N(C)C)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 160, 60, 60, 60, 60, 60, 44, 44, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 44, 22, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 60] 201
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, 42, 43, 44, 45, 46])
total number of confs: 508
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078965 none CC(OC1=CC=CC(C=NNCC2=CC=CC=C2N(C)C)=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 24, 60, 60, 60, 60, 60, 60, 60, 60, 1, 24, 33, 33, 24, 24, 24, 24, 1, 1, 1, 5, 8, 24, 24, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 46, 21, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 244
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078965 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078965
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078965/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078965
Building REAL300000078966
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078966'
/scratch/stefan/7769659/working/building/REAL300000078966 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078966

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078966/0 /scratch/stefan/7769659/working/building/REAL300000078966 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1028
`/scratch/stefan/7769659/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCCC(=O)[O-])=C1)

`REAL300000078966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078966 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 58, 58, 57, 58, 58, 36, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 19, 22, 32, 29, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 36, 36, 10, 6, 1, 1, 1, 19, 19, 22, 22, 1] 201
rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45])
total number of confs: 271
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078966 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 16, 31, 31, 58, 58, 58, 58, 58, 157, 196, 201, 201, 201, 58, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 16, 31, 58, 58, 58, 196, 196, 201, 201, 58] 201
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, 42, 43, 44, 45, 46])
total number of confs: 492
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078966 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078966
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078966/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078966
Building REAL300000078967
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078967'
/scratch/stefan/7769659/working/building/REAL300000078967 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078967

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078967/0 /scratch/stefan/7769659/working/building/REAL300000078967 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1029
`/scratch/stefan/7769659/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1)

`REAL300000078967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078967 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [106, 106, 106, 106, 106, 106, 106, 106, 67, 24, 6, 6, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 67, 67, 24, 6, 1, 1, 5, 5, 1] 136
rigid atoms, others: [45, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44])
total number of confs: 327
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078967 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 50, 50, 106, 106, 59, 87, 136, 136, 136, 136, 106, 106, 106, 106, 106, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 21, 50, 106, 106, 136, 136, 106] 136
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 441
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078967 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078967
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078967/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078967
Building REAL300000078968
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078968'
/scratch/stefan/7769659/working/building/REAL300000078968 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078968

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078968/0 /scratch/stefan/7769659/working/building/REAL300000078968 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1030
`/scratch/stefan/7769659/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCC(=O)[O-])=C1)

`REAL300000078968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078968 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 62, 63, 63, 34, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 18, 27, 27, 1, 63, 63, 63, 63, 63, 63, 63, 62, 63, 63, 34, 34, 9, 4, 1, 1, 1, 18, 18, 1] 201
rigid atoms, others: [38, 39, 40, 43, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42])
total number of confs: 256
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078968 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 19, 37, 37, 63, 63, 63, 63, 63, 138, 201, 201, 201, 63, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 19, 37, 63, 63, 63, 201, 201, 63] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 566
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078968 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078968
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078968/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078968
Building REAL300000078969
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078969'
/scratch/stefan/7769659/working/building/REAL300000078969 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078969

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078969/0 /scratch/stefan/7769659/working/building/REAL300000078969 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1031
`/scratch/stefan/7769659/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C(OCC(=O)[O-])=C1)

`REAL300000078969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078969 none COC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 65, 80, 80, 65, 65, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 80, 80, 145, 201, 201, 201, 80, 89, 89, 89, 80, 80, 65, 27, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 201, 201, 80] 201
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 631
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078969 none COC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C(OCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 10, 39, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 7, 31, 48, 48, 1, 3, 3, 3, 1, 1, 4, 10, 39, 39, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 31, 31, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 19, 20, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 360
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078969 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078969
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078969/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078969
Building REAL300000078970
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078970'
/scratch/stefan/7769659/working/building/REAL300000078970 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078970

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078970/0 /scratch/stefan/7769659/working/building/REAL300000078970 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1032
`/scratch/stefan/7769659/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)

`REAL300000078970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078970 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OC(F)(F)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.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 8, 4, 4, 1, 1, 1, 1, 1, 1, 12, 39, 39, 38, 53, 53, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 8, 4, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078970 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(OC(F)(F)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.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 26, 26, 32, 32, 26, 26, 121, 201, 201, 201, 201, 201, 32, 32, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 17, 26, 32, 32, 32, 32] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 35, 33] set([10, 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])
total number of confs: 635
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078970 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078970
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078970/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078970
Building REAL300000078971
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078971'
/scratch/stefan/7769659/working/building/REAL300000078971 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078971

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078971/0 /scratch/stefan/7769659/working/building/REAL300000078971 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1033
`/scratch/stefan/7769659/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=C(Br)C=C(C(=O)[O-])N1C)

`REAL300000078971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078971 none CN(C)C1=CC=CC=C1CNN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [161, 161, 161, 161, 161, 161, 161, 161, 106, 64, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 106, 106, 64, 13, 1, 2, 2, 2] 161
rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 441
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078971 none CN(C)C1=CC=CC=C1CNN=CC1=C(Br)C=C(C(=O)[O-])N1C NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 29, 107, 107, 161, 161, 161, 161, 161, 161, 161, 161, 161, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 29, 107, 161, 161, 161, 161] 161
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 290
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078971 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078971
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078971/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078971
Building REAL300000078972
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078972'
/scratch/stefan/7769659/working/building/REAL300000078972 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078972

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078972/0 /scratch/stefan/7769659/working/building/REAL300000078972 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1034
`/scratch/stefan/7769659/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC=C2N(C)C)C=C1)

`REAL300000078972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078972 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC=C2N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201, 201, 201, 201, 141, 31, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 201, 201] 201
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, 43, 44, 45, 46])
total number of confs: 335
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078972 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNCC2=CC=CC=C2N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 34, 115, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 6, 34, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 45, 46, 25, 26, 30] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 536
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078972 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078972
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078972/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078972
Building REAL300000078973
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078973'
/scratch/stefan/7769659/working/building/REAL300000078973 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000078973

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078973/0 /scratch/stefan/7769659/working/building/REAL300000078973 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1035
`/scratch/stefan/7769659/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1)

`REAL300000078973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078973 none CN(C)C1=CC=CC=C1CNN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 113, 71, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 71, 71, 30, 6, 1, 1, 1, 1] 113
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 311
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078973 none CN(C)C1=CC=CC=C1CNN=CC1=C2C=CC(C(=O)[O-])=CC2=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 30, 99, 99, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 30, 99, 113, 113, 113, 113] 113
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, 42])
total number of confs: 219
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078973 /scratch/stefan/7769659/working /scratch/stefan/7769659
mkdir: created directory `1'
/scratch/stefan/7769659/working/building/REAL300000078973/1 /scratch/stefan/7769659/working/building/REAL300000078973 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 1 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1036
`/scratch/stefan/7769659/working/3D/1036' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=NNC2=CC(C(=O)[O-])=CC=C12)

`REAL300000078973.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000078973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078973/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078973 none CN(C)C1=CC=CC=C1CNN=CC1=NNC2=CC(C(=O)[O-])=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 132, 66, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 66, 12, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 562
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078973 none CN(C)C1=CC=CC=C1CNN=CC1=NNC2=CC(C(=O)[O-])=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 33, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 33, 105, 201, 201, 201, 201] 201
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, 42])
total number of confs: 349
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078973 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078973
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078973/0.*
1: /scratch/stefan/7769659/working/building/REAL300000078973/1.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078973
Building REAL300000078974
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078974'
/scratch/stefan/7769659/working/building/REAL300000078974 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078974

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078974/0 /scratch/stefan/7769659/working/building/REAL300000078974 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1037
`/scratch/stefan/7769659/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])N=N1)

`REAL300000078974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078974 none CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 108, 76, 32, 6, 6, 1, 1, 1, 1, 1, 8, 16, 16, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 76, 76, 31, 6, 1, 8, 8] 201
rigid atoms, others: [36, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 354
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078974 none CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 69, 69, 108, 108, 108, 201, 201, 201, 108, 108, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 24, 69, 108, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([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: 692
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078974 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078974
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078974/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078974
Building REAL300000078975
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078975'
/scratch/stefan/7769659/working/building/REAL300000078975 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078975

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078975/0 /scratch/stefan/7769659/working/building/REAL300000078975 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1038
`/scratch/stefan/7769659/working/3D/1038' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCC(=O)[O-])

`REAL300000078975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078975 none COC1=CC(C=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 59, 59, 59, 26, 26, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 59, 59, 59, 59, 125, 189, 189, 201, 189, 86, 86, 86, 59, 26, 16, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 59, 59, 189, 189, 189, 189] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 650
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078975 none COC1=CC(C=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 11, 38, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 7, 12, 12, 24, 22, 3, 3, 3, 1, 7, 11, 38, 38, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 12, 12, 12, 12] 201
rigid atoms, others: [1, 2, 3, 4, 5, 45, 46, 18, 19, 20, 21, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078975 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078975
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078975/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078975
Building REAL300000078976
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078976'
/scratch/stefan/7769659/working/building/REAL300000078976 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078976

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078976/0 /scratch/stefan/7769659/working/building/REAL300000078976 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1039
`/scratch/stefan/7769659/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C=C1Cl)

`REAL300000078976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078976 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 94, 56, 33, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 56, 56, 33, 10, 1, 1, 1] 94
rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 244
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078976 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 28, 82, 82, 94, 94, 82, 94, 94, 94, 94, 94, 94, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 28, 82, 94, 94, 94] 94
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 243
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078976 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078976
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078976/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078976
Building REAL300000078977
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078977'
/scratch/stefan/7769659/working/building/REAL300000078977 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078977

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078977/0 /scratch/stefan/7769659/working/building/REAL300000078977 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1040
`/scratch/stefan/7769659/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(O)C(C(=O)[O-])=C1)

`REAL300000078977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078977 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(O)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 47, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 47, 47, 23, 9, 1, 1, 2, 1] 176
rigid atoms, others: [37, 38, 40, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 239
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078977 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(O)C(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 26, 68, 68, 88, 88, 88, 88, 88, 88, 88, 88, 88, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 26, 68, 88, 88, 176, 88] 176
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 361
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078977 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078977
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078977/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078977
Building REAL300000078978
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078978'
/scratch/stefan/7769659/working/building/REAL300000078978 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078978

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078978/0 /scratch/stefan/7769659/working/building/REAL300000078978 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1041
`/scratch/stefan/7769659/working/3D/1041' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C=C1)C(=O)[O-])

`REAL300000078978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078978 none CC(OC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 170, 79, 49, 97, 97, 49, 49, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 97, 97, 201, 201, 201, 201, 201, 201, 201, 97, 97, 49, 24, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 97, 97] 201
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 685
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078978 none CC(OC1=CC=C(C=NNCC2=CC=CC=C2N(C)C)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 12, 43, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 14, 19, 19, 14, 14, 14, 14, 1, 1, 6, 12, 43, 43, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 45, 46, 20, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 295
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078978 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078978
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078978/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078978
Building REAL300000078979
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078979'
/scratch/stefan/7769659/working/building/REAL300000078979 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078979

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078979/0 /scratch/stefan/7769659/working/building/REAL300000078979 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1042
`/scratch/stefan/7769659/working/3D/1042' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12)

`REAL300000078979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078979 none CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 132, 132, 132, 132, 132, 132, 132, 77, 23, 7, 7, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 77, 77, 23, 7, 1, 8, 8, 1, 1, 1, 1] 201
rigid atoms, others: [45, 40, 44, 43, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 406
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078979 none CN(C)C1=CC=CC=C1CNN=CC1=CN(CC(=O)[O-])C2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 71, 71, 132, 132, 132, 201, 201, 201, 132, 132, 132, 132, 132, 132, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 27, 71, 132, 201, 201, 132, 132, 132, 132] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 35, 33] set([10, 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])
total number of confs: 609
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078979 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078979
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078979/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078979
Building REAL300000078980
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078980'
/scratch/stefan/7769659/working/building/REAL300000078980 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078980

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078980/0 /scratch/stefan/7769659/working/building/REAL300000078980 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1043
`/scratch/stefan/7769659/working/3D/1043' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC=C2N(C)C)N1)

`REAL300000078980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078980 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC=C2N(C)C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 130, 130, 130, 130, 103, 103, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 130, 130, 130, 130, 130, 103, 31, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 130] 130
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 239
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078980 none CC1=C(C(=O)[O-])C=C(C=NNCC2=CC=CC=C2N(C)C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 25, 74, 130, 130, 130, 130, 130, 130, 130, 130, 1, 2, 2, 2, 1, 8, 25, 74, 74, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1] 130
rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 40, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 353
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078980 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078980
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078980/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078980
Building REAL300000078981
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078981'
/scratch/stefan/7769659/working/building/REAL300000078981 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078981

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078981/0 /scratch/stefan/7769659/working/building/REAL300000078981 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1044
`/scratch/stefan/7769659/working/3D/1044' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000078981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078981 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 13, 25, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 18, 28, 41, 55, 55, 1, 9, 9, 9, 13, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 18, 18, 28, 28, 41, 41, 1] 201
rigid atoms, others: [1, 43, 44, 45, 14, 15, 16, 17, 18, 19, 52, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51])
total number of confs: 324
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078981 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 31, 31, 31, 31, 31, 81, 115, 135, 201, 201, 201, 31, 13, 13, 13, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 31, 31, 31, 115, 115, 135, 135, 201, 201, 31] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 787
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078981 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078981
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078981/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078981
Building REAL300000078982
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078982'
/scratch/stefan/7769659/working/building/REAL300000078982 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078982

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078982/0 /scratch/stefan/7769659/working/building/REAL300000078982 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1045
`/scratch/stefan/7769659/working/3D/1045' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C)

`REAL300000078982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078982 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 71, 74, 74, 74, 74, 74, 74, 198, 201, 201, 201, 201, 74, 74, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 71, 71, 71, 71, 74, 74, 74, 74, 74, 74, 201, 201, 201, 201, 74, 74, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54, 55])
total number of confs: 452
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078982 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 8, 17, 17, 20, 20, 1, 1, 3, 9, 9, 31, 74, 74, 74, 74, 74, 74, 74, 74, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 17, 17, 17, 17, 1, 1, 31, 31, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 239
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078982 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078982
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078982/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078982
Building REAL300000078983
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078983'
/scratch/stefan/7769659/working/building/REAL300000078983 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078983

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078983/0 /scratch/stefan/7769659/working/building/REAL300000078983 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1046
`/scratch/stefan/7769659/working/3D/1046' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C)

`REAL300000078983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078983 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 31, 70, 86, 86, 86, 86, 86, 86, 194, 201, 201, 201, 86, 86, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 70, 70, 70, 70, 86, 86, 86, 86, 86, 86, 201, 201, 86, 86, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078983 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 18, 18, 1, 1, 3, 10, 10, 38, 86, 86, 86, 86, 86, 86, 86, 86, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 12, 12, 1, 1, 38, 38, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 39, 13, 14, 40, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078983 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078983
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078983/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078983
Building REAL300000078984
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078984'
/scratch/stefan/7769659/working/building/REAL300000078984 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078984

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078984/0 /scratch/stefan/7769659/working/building/REAL300000078984 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1047
`/scratch/stefan/7769659/working/3D/1047' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000078984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078984 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 12, 32, 70, 70, 66, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 9, 19, 19, 27, 27, 1, 6, 6, 6, 12, 32, 32, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 19, 19, 19, 19, 1] 201
rigid atoms, others: [1, 49, 42, 43, 44, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48])
total number of confs: 289
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078984 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 70, 70, 70, 70, 70, 151, 201, 201, 201, 201, 70, 34, 34, 34, 20, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 70, 70, 70, 201, 201, 201, 201, 70] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 564
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078984 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078984
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078984/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078984
Building REAL300000078985
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078985'
/scratch/stefan/7769659/working/building/REAL300000078985 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078985

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078985/0 /scratch/stefan/7769659/working/building/REAL300000078985 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1048
`/scratch/stefan/7769659/working/3D/1048' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C)

`REAL300000078985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078985 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 29, 57, 61, 61, 61, 61, 61, 61, 201, 201, 201, 201, 201, 61, 61, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 57, 57, 57, 57, 61, 61, 61, 61, 61, 61, 201, 201, 201, 201, 61, 61, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54, 55])
total number of confs: 393
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078985 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 14, 14, 1, 1, 3, 8, 8, 29, 61, 61, 61, 61, 61, 61, 61, 61, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 7, 7, 7, 7, 1, 1, 29, 29, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61] 201
rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 186
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078985 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078985
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078985/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078985
Building REAL300000078986
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078986'
/scratch/stefan/7769659/working/building/REAL300000078986 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078986

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078986/0 /scratch/stefan/7769659/working/building/REAL300000078986 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1049
`/scratch/stefan/7769659/working/3D/1049' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNCC1=CC=CC=C1N(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000078986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078986 none CCC(=NNCC1=CC=CC=C1N(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 6, 6, 15, 38, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 21, 21, 1, 1, 7, 7, 7, 7, 7, 15, 38, 38, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 6, 6, 14, 14, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [48, 2, 27, 47, 16, 17, 18, 19, 57, 58, 15, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 246
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078986 none CCC(=NNCC1=CC=CC=C1N(C)C)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 24, 24, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 24, 57, 57, 24, 24, 125, 153, 188, 188, 188, 180, 194, 57, 57, 35, 35, 35, 35, 35, 11, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 57, 57, 153, 153, 188, 188, 188, 188, 188, 188, 57, 57] 201
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58])
total number of confs: 723
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078986 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078986
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078986/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078986
Building REAL300000078987
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078987'
/scratch/stefan/7769659/working/building/REAL300000078987 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078987

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078987/0 /scratch/stefan/7769659/working/building/REAL300000078987 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1050
`/scratch/stefan/7769659/working/3D/1050' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC=C1N(C)C)C1=CSC(C(=O)[O-])=C1)

`REAL300000078987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078987 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 48, 95, 154, 154, 153, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 48, 95, 95, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1] 154
rigid atoms, others: [1, 38, 39, 14, 15, 16, 17, 18, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 455
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078987 none CC(=NNCC1=CC=CC=C1N(C)C)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 84, 154, 154, 154, 154, 154, 154, 154, 84, 84, 84, 31, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 154, 154] 154
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 286
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078987 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078987
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078987/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078987
Building REAL300000078988
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078988'
/scratch/stefan/7769659/working/building/REAL300000078988 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078988

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078988/0 /scratch/stefan/7769659/working/building/REAL300000078988 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1051)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1051
`/scratch/stefan/7769659/working/3D/1051' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=C1CC(C(=O)[O-])(C2=CC=CC=C2)C1)

`REAL300000078988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078988 none CN(C)C1=CC=CC=C1CNN=C1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 140, 141, 140, 140, 88, 140, 140, 53, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 1, 7, 7, 1, 141, 141, 141, 141, 141, 141, 140, 140, 140, 140, 53, 53, 10, 1, 1, 7, 7, 1, 7, 7, 1, 1] 201
rigid atoms, others: [45, 38, 39, 10, 11, 12, 13, 14, 15, 18, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 524
number of broken/clashed sets: 171
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078988 none CN(C)C1=CC=CC=C1CNN=C1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 36, 140, 140, 140, 140, 197, 197, 140, 201, 201, 140, 201, 201, 140, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 36, 140, 140, 201, 201, 140, 201, 201, 140, 140] 201
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, 42, 43, 44, 45, 46])
total number of confs: 777
number of broken/clashed sets: 171
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078988 none CN(C)C1=CC=CC=C1CNN=C1CC(C(=O)[O-])(C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 154, 201, 201, 106, 37, 7, 7, 7, 7, 1, 7, 10, 10, 1, 1, 1, 1, 1, 1, 7, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 37, 7, 7, 1, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [40, 41, 42, 43, 44, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46])
total number of confs: 728
number of broken/clashed sets: 171
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078988 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078988
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078988/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078988
Building REAL300000078989
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078989'
/scratch/stefan/7769659/working/building/REAL300000078989 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078989

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078989/0 /scratch/stefan/7769659/working/building/REAL300000078989 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1052)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1052
`/scratch/stefan/7769659/working/3D/1052' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NCC1=CC=CC=C1N(C)C)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000078989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078989 none CC(N=NCC1=CC=CC=C1N(C)C)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 16, 16, 73, 154, 154, 100, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 3, 3, 3, 3, 73, 73, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 6, 6, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [1, 42, 43, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 599
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078989 none CC(N=NCC1=CC=CC=C1N(C)C)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [140, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 140, 154, 154, 154, 154, 154, 201, 201, 201, 154, 154, 154, 140, 140, 140, 140, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 154, 154, 201, 201, 154, 154, 154, 154, 154, 154] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 814
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078989 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078989
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078989/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078989
Building REAL300000078990
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078990'
/scratch/stefan/7769659/working/building/REAL300000078990 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078990

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078990/0 /scratch/stefan/7769659/working/building/REAL300000078990 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1053)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1053
`/scratch/stefan/7769659/working/3D/1053' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])=NNCC1=CC=CC=C1N(C)C)

`REAL300000078990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078990 none CC(CCCCCCC(=O)[O-])=NNCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 115, 112, 133, 113, 134, 201, 201, 201, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 36, 36, 36, 115, 115, 133, 133, 133, 133, 134, 134, 134, 134, 201, 201, 14, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50])
total number of confs: 1158
number of broken/clashed sets: 131
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078990 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078990
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078990/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078990
Building REAL300000078991
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078991'
/scratch/stefan/7769659/working/building/REAL300000078991 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078991

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078991/0 /scratch/stefan/7769659/working/building/REAL300000078991 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1054)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1054
`/scratch/stefan/7769659/working/3D/1054' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C)

`REAL300000078991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078991 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [98, 98, 98, 98, 135, 135, 135, 98, 98, 39, 38, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 98, 98, 98, 98, 98, 135, 135, 98, 98, 98, 98, 98, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 135
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 444
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078991 none CC1C(CC(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 8, 13, 13, 1, 1, 1, 1, 8, 8, 46, 98, 98, 98, 98, 98, 98, 100, 100, 2, 2, 2, 1, 1, 8, 8, 1, 1, 1, 1, 1, 46, 46, 98, 98, 98, 98, 100, 100, 100, 100, 100, 100] 135
rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 25, 26, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 281
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078991 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078991
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078991/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078991
Building REAL300000078992
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078992'
/scratch/stefan/7769659/working/building/REAL300000078992 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078992

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078992/0 /scratch/stefan/7769659/working/building/REAL300000078992 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1055)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1055
`/scratch/stefan/7769659/working/3D/1055' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NCC2=CC=CC=C2N(C)C)CCC(C(=O)[O-])C1(C)C)

`REAL300000078992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078992 none CC1C(N=NCC2=CC=CC=C2N(C)C)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70] 70
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 176
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078992 none CC1C(N=NCC2=CC=CC=C2N(C)C)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 40, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 70
rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49, 50, 51])
total number of confs: 184
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078992 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078992
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078992/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078992
Building REAL300000078993
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078993'
/scratch/stefan/7769659/working/building/REAL300000078993 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078993

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078993/0 /scratch/stefan/7769659/working/building/REAL300000078993 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1056)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1056
`/scratch/stefan/7769659/working/3D/1056' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C)

`REAL300000078993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078993 none CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 69, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 69
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 187
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078993 none CC1CC(C(=O)[O-])CCC1N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 6, 6, 32, 69, 69, 41, 69, 69, 69, 69, 69, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69] 69
rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 32, 25, 26, 27, 28, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 275
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078993 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078993
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078993/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078993
Building REAL300000078994
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078994'
/scratch/stefan/7769659/working/building/REAL300000078994 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078994

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078994/0 /scratch/stefan/7769659/working/building/REAL300000078994 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1057)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1057
`/scratch/stefan/7769659/working/3D/1057' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NCC2=CC=CC=C2N(C)C)CCC1C(=O)[O-])

`REAL300000078994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078994 none CC1CC(N=NCC2=CC=CC=C2N(C)C)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 76, 76, 76, 76, 76] 76
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 192
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078994 none CC1CC(N=NCC2=CC=CC=C2N(C)C)CCC1C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 13, 13, 47, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 1, 47, 47, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1] 76
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 43, 44, 45, 16, 17, 18, 19, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 211
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078994 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078994
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078994/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078994
Building REAL300000078995
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078995'
/scratch/stefan/7769659/working/building/REAL300000078995 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078995

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078995/0 /scratch/stefan/7769659/working/building/REAL300000078995 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1058)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1058
`/scratch/stefan/7769659/working/3D/1058' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCCC(=O)[O-])

`REAL300000078995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078995 none COC1=CC(C(C)=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 64, 64, 29, 29, 29, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 64, 64, 64, 64, 127, 187, 187, 201, 201, 201, 103, 103, 103, 64, 29, 29, 29, 12, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 64, 64, 187, 187, 187, 187, 201, 201] 201
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 657
number of broken/clashed sets: 133
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078995 none COC1=CC(C(C)=NNCC2=CC=CC=C2N(C)C)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 47, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 5, 11, 12, 19, 28, 28, 3, 3, 3, 1, 7, 7, 7, 19, 47, 47, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 11, 11, 11, 11, 19, 19] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 49, 50, 19, 20, 21, 22] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56])
total number of confs: 312
number of broken/clashed sets: 133
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078995 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078995
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078995/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078995
Building REAL300000078996
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078996'
/scratch/stefan/7769659/working/building/REAL300000078996 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078996

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078996/0 /scratch/stefan/7769659/working/building/REAL300000078996 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1059)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1059
`/scratch/stefan/7769659/working/3D/1059' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC=C1N(C)C)

`REAL300000078996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078996 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [151, 45, 151, 193, 201, 201, 201, 201, 201, 201, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 151, 151, 151, 151, 193, 193, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 769
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078996 none CC(CC1(C(=O)[O-])CCC1)N=NCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 1, 1, 1, 3, 3, 1, 1, 1, 7, 27, 27, 107, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 503
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078996 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078996
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078996/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078996
Building REAL300000078997
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078997'
/scratch/stefan/7769659/working/building/REAL300000078997 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078997

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078997/0 /scratch/stefan/7769659/working/building/REAL300000078997 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1060)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1060
`/scratch/stefan/7769659/working/3D/1060' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNCC1=CC=CC=C1N(C)C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1)

`REAL300000078997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078997 none CC(=NNCC1=CC=CC=C1N(C)C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 45, 136, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 1, 1, 2, 2, 2, 1] 201
rigid atoms, others: [1, 47, 46, 14, 15, 16, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50])
total number of confs: 605
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078997 none CC(=NNCC1=CC=CC=C1N(C)C)C1=C(CC(=O)[O-])C2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 31, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 345
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078997 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078997
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078997/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078997
Building REAL300000078998
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078998'
/scratch/stefan/7769659/working/building/REAL300000078998 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078998

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078998/0 /scratch/stefan/7769659/working/building/REAL300000078998 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1061)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1061
`/scratch/stefan/7769659/working/3D/1061' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC=C1N(C)C)

`REAL300000078998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078998 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201, 201, 201, 201, 201, 201, 109, 31, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 338
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078998 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNCC1=CC=CC=C1N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 2, 2, 1, 1, 1, 13, 13, 67, 127, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 13, 67, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 568
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078998 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078998
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078998/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078998
Building REAL300000078999
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000078999'
/scratch/stefan/7769659/working/building/REAL300000078999 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000078999

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000078999/0 /scratch/stefan/7769659/working/building/REAL300000078999 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1062)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1062
`/scratch/stefan/7769659/working/3D/1062' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(C(=O)[O-])=C1Cl)

`REAL300000078999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000078999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000078999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078999 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(C(=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 100, 61, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 61, 61, 23, 6, 1, 1, 1] 100
rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 294
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000078999 none CN(C)C1=CC=CC=C1CNN=CC1=CC=CC(C(=O)[O-])=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 27, 71, 71, 100, 100, 100, 100, 100, 100, 100, 100, 100, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 27, 71, 100, 100, 100] 100
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 203
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000078999 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000078999
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000078999/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000078999
Building REAL300000079000
mkdir: created directory `/scratch/stefan/7769659/working/building/REAL300000079000'
/scratch/stefan/7769659/working/building/REAL300000079000 /scratch/stefan/7769659/working /scratch/stefan/7769659
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000079000

mkdir: created directory `0'
/scratch/stefan/7769659/working/building/REAL300000079000/0 /scratch/stefan/7769659/working/building/REAL300000079000 /scratch/stefan/7769659/working /scratch/stefan/7769659
Protomer 0 (index: 1063)
Found valid previously generated 3D confromation in /scratch/stefan/7769659/working/3D/1063
`/scratch/stefan/7769659/working/3D/1063' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C(F)=C1)

`REAL300000079000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000079000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769659/working/building/REAL300000079000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000079000 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 105, 42, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 42, 12, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 514
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000079000 none CN(C)C1=CC=CC=C1CNN=CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 31, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 31, 98, 201, 201, 201] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 382
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769659/working/building/REAL300000079000 /scratch/stefan/7769659/working /scratch/stefan/7769659

Finished preparing REAL300000079000
Recording results
/scratch/stefan/7769659/working /scratch/stefan/7769659
Appending to /scratch/stefan/7769659/finished/xaaaada.*
0: /scratch/stefan/7769659/working/building/REAL300000079000/0.*
Removing working files in /scratch/stefan/7769659/working/building/REAL300000079000
/scratch/stefan/7769659
Compressing combined databse files
/scratch/stefan/7769659/finished/xaaaada.db2.gz
/scratch/stefan/7769659/finished/xaaaada.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7769659/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7769659/working/3D/1064'
removed directory: `/scratch/stefan/7769659/working/3D'
`/scratch/stefan/7769659/working/protonate' -> `/scratch/stefan/7769659/archive'
`/scratch/stefan/7769659/working/input-smiles.ism' -> `/scratch/stefan/7769659/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7769659/working/building'
rmdir: removing directory, `/scratch/stefan/7769659/working'
ls: No match.
ls: No match.